<?xml version="1.0" encoding="US-ASCII"?>
<!-- Generated by Broadridge Transform (tm) - http://www.broadridge.com -->
<!-- Created: Wed Jul 29 21:05:17 UTC 2026 -->
<linkbase xmlns="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ConsolidatedBalanceSheet" roleURI="http://ionis.com/role/ConsolidatedBalanceSheet"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ConsolidatedBalanceSheet_Parentheticals" roleURI="http://ionis.com/role/ConsolidatedBalanceSheet_Parentheticals"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ConsolidatedIncomeStatement" roleURI="http://ionis.com/role/ConsolidatedIncomeStatement"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ConsolidatedComprehensiveIncome" roleURI="http://ionis.com/role/ConsolidatedComprehensiveIncome"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ShareholdersEquityType2or3" roleURI="http://ionis.com/role/ShareholdersEquityType2or3"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ShareholdersEquityType2or3_Parentheticals" roleURI="http://ionis.com/role/ShareholdersEquityType2or3_Parentheticals"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ConsolidatedCashFlow" roleURI="http://ionis.com/role/ConsolidatedCashFlow"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ConsolidatedCashFlow_Parentheticals" roleURI="http://ionis.com/role/ConsolidatedCashFlow_Parentheticals"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_OrganizationandBasisofPresentation" roleURI="http://ionis.com/role/OrganizationandBasisofPresentation"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_SignificantAccountingPolicies" roleURI="http://ionis.com/role/SignificantAccountingPolicies"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_SupplementalFinancialData" roleURI="http://ionis.com/role/SupplementalFinancialData"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_Revenues" roleURI="http://ionis.com/role/Revenues"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_CollaborativeArrangementsandLicensingAgreements" roleURI="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreements"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_BasicandDilutedNetIncomeLossPerShare" roleURI="http://ionis.com/role/BasicandDilutedNetIncomeLossPerShare"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_Investments" roleURI="http://ionis.com/role/Investments"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_FairValueMeasurements" roleURI="http://ionis.com/role/FairValueMeasurements"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_StockbasedCompensationExpense" roleURI="http://ionis.com/role/StockbasedCompensationExpense"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_LiabilityRelatedtoSaleofFutureRoyalties" roleURI="http://ionis.com/role/LiabilityRelatedtoSaleofFutureRoyalties"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ConvertibleDebt" roleURI="http://ionis.com/role/ConvertibleDebt"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_LegalProceedings" roleURI="http://ionis.com/role/LegalProceedings"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_SegmentInformation" roleURI="http://ionis.com/role/SegmentInformation"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_AccountingPoliciesByPolicy" roleURI="http://ionis.com/role/AccountingPoliciesByPolicy"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_SupplementalFinancialDataTables" roleURI="http://ionis.com/role/SupplementalFinancialDataTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_RevenuesTables" roleURI="http://ionis.com/role/RevenuesTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_CollaborativeArrangementsandLicensingAgreementsTables" roleURI="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_BasicandDilutedNetIncomeLossPerShareTables" roleURI="http://ionis.com/role/BasicandDilutedNetIncomeLossPerShareTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_InvestmentsTables" roleURI="http://ionis.com/role/InvestmentsTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_FairValueMeasurementsTables" roleURI="http://ionis.com/role/FairValueMeasurementsTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_StockbasedCompensationExpenseTables" roleURI="http://ionis.com/role/StockbasedCompensationExpenseTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_LiabilityRelatedtoSaleofFutureRoyaltiesTables" roleURI="http://ionis.com/role/LiabilityRelatedtoSaleofFutureRoyaltiesTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ConvertibleDebtTables" roleURI="http://ionis.com/role/ConvertibleDebtTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_SegmentInformationTables" roleURI="http://ionis.com/role/SegmentInformationTables"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_InventoriesTable" roleURI="http://ionis.com/role/InventoriesTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_AccruedLiabilitiesTable" roleURI="http://ionis.com/role/AccruedLiabilitiesTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_RevenuesTable" roleURI="http://ionis.com/role/RevenuesTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_RevenuefromCollaborativeRelationshipwithBiogenTable" roleURI="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithBiogenTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_RevenuefromCollaborativeRelationshipwithGSKTable" roleURI="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithGSKTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_RevenuefromCollaborativeRelationshipwithOnoTable" roleURI="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithOnoTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_RevenuefromCollaborativeRelationshipwithOtsukaTable" roleURI="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithOtsukaTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_RevenuefromCollaborativeRelationshipwithRecordatiTable" roleURI="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithRecordatiTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_RevenuefromCollaborativeRelationshipwithRocheTable" roleURI="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithRocheTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_DilutedNetIncomePerShareTable" roleURI="http://ionis.com/role/DilutedNetIncomePerShareTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ContractMaturityofAvailableforSaleSecuritiesTable" roleURI="http://ionis.com/role/ContractMaturityofAvailableforSaleSecuritiesTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_SummaryofInvestmentsTable" roleURI="http://ionis.com/role/SummaryofInvestmentsTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_TemporarilyImpairedInvestmentsTable" roleURI="http://ionis.com/role/TemporarilyImpairedInvestmentsTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_AssetsMeasuredatFairValueonaRecurringBasisTable" roleURI="http://ionis.com/role/AssetsMeasuredatFairValueonaRecurringBasisTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_StockbasedCompensationExpenseTable" roleURI="http://ionis.com/role/StockbasedCompensationExpenseTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_WeightedAverageAssumptionsforStockOptionsTable" roleURI="http://ionis.com/role/WeightedAverageAssumptionsforStockOptionsTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_WeightedAverageAssumptionsforESPPTable" roleURI="http://ionis.com/role/WeightedAverageAssumptionsforESPPTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_LiabilityRelatedtoSaleofFutureRoyaltiesTable" roleURI="http://ionis.com/role/LiabilityRelatedtoSaleofFutureRoyaltiesTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_0Notesdue2030Table" roleURI="http://ionis.com/role/0Notesdue2030Table"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_175Notesdue2028Table" roleURI="http://ionis.com/role/175Notesdue2028Table"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_SegmentInformationTable" roleURI="http://ionis.com/role/SegmentInformationTable"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_OrganizationandBasisofPresentationDetails" roleURI="http://ionis.com/role/OrganizationandBasisofPresentationDetails"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_RevenuesDetails" roleURI="http://ionis.com/role/RevenuesDetails"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_CollaborativeArrangementsandLicensingAgreementsDetailsBiogen" roleURI="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsBiogen"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_CollaborativeArrangementsandLicensingAgreementsDetailsGSK" roleURI="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsGSK"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_CollaborativeArrangementsandLicensingAgreementsDetailsOno" roleURI="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsOno"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_CollaborativeArrangementsandLicensingAgreementsDetailsOtsuka" roleURI="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsOtsuka"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_CollaborativeArrangementsandLicensingAgreementsDetailsRecordati" roleURI="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsRecordati"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_CollaborativeArrangementsandLicensingAgreementsDetailsRoche" roleURI="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsRoche"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_BasicandDilutedNetIncomeLossPerShareDetails" roleURI="http://ionis.com/role/BasicandDilutedNetIncomeLossPerShareDetails"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_InvestmentsDetails" roleURI="http://ionis.com/role/InvestmentsDetails"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_FairValueMeasurementsDetails" roleURI="http://ionis.com/role/FairValueMeasurementsDetails"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_StockbasedCompensationExpenseDetails" roleURI="http://ionis.com/role/StockbasedCompensationExpenseDetails"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_LiabilityRelatedtoSaleofFutureRoyaltiesDetails" roleURI="http://ionis.com/role/LiabilityRelatedtoSaleofFutureRoyaltiesDetails"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_ConvertibleDebtDetails" roleURI="http://ionis.com/role/ConvertibleDebtDetails"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#ions_r_SegmentInformationDetails" roleURI="http://ionis.com/role/SegmentInformationDetails"/>
  <roleRef xlink:type="simple" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#InsiderTradingArrangements" roleURI="http://xbrl.sec.gov/ecd/role/InsiderTradingArrangements"/>
  <roleRef xlink:type="simple" xlink:href="ions-20260630.xsd#DocumentAndEntityInformation" roleURI="http://ionis.com/role/DocumentAndEntityInformation"/>
  <presentationLink xlink:role="http://ionis.com/role/ConsolidatedBalanceSheet" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfFinancialPositionAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfFinancialPositionAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_StatementTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_DebtInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentNameDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentNameDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="us-gaap_DebtInstrumentNameDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2030Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2030Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2030Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2028Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2028Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2028Member" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AssetsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AssetsAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AssetsAbstract" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AssetsCurrentAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AssetsCurrentAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_AssetsCurrentAbstract" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShortTermInvestments" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShortTermInvestments"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_ShortTermInvestments" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerAssetNetCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerAssetNetCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_ContractWithCustomerAssetNetCurrent" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InventoryNet" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InventoryNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_InventoryNet" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherAssetsCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherAssetsCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_OtherAssetsCurrent" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AssetsCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AssetsCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherAssetsCurrent" xlink:to="us-gaap_AssetsCurrent" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseRightOfUseAsset"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherAssetsNoncurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherAssetsNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_OtherAssetsNoncurrent" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_Assets" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Assets"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherAssetsNoncurrent" xlink:to="us-gaap_Assets" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesAndStockholdersEquityAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_LiabilitiesAndStockholdersEquityAbstract" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_LiabilitiesCurrentAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesCurrentAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesCurrentAbstract" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AccountsPayableCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccountsPayableCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_AccountsPayableCurrent" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeRelatedLiabilitiesCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeRelatedLiabilitiesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_EmployeeRelatedLiabilitiesCurrent" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AccruedLiabilitiesCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccruedLiabilitiesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_AccruedLiabilitiesCurrent" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AccruedIncomeTaxesCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccruedIncomeTaxesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_AccruedIncomeTaxesCurrent" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConvertibleDebtCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConvertibleDebtCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_ConvertibleDebtCurrent" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiabilityCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerLiabilityCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_ContractWithCustomerLiabilityCurrent" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherLiabilitiesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_OtherLiabilitiesCurrent" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_LiabilitiesCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherLiabilitiesCurrent" xlink:to="us-gaap_LiabilitiesCurrent" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiabilityNoncurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerLiabilityNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_ContractWithCustomerLiabilityNoncurrent" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConvertibleDebtNoncurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConvertibleDebtNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_ConvertibleDebtNoncurrent" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="LiabilityRelatedToSaleOfFutureRoyaltiesNetNoncurrent" xlink:href="ions-20260630.xsd#ions_LiabilityRelatedToSaleOfFutureRoyaltiesNetNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="LiabilityRelatedToSaleOfFutureRoyaltiesNetNoncurrent" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesNoncurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherLiabilitiesNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_OtherLiabilitiesNoncurrent" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_Liabilities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Liabilities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherLiabilitiesNoncurrent" xlink:to="us-gaap_Liabilities" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StockholdersEquityAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockholdersEquityAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_StockholdersEquityAbstract" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CommonStockValue" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockValue"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_CommonStockValue" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AdditionalPaidInCapitalCommonStock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_AdditionalPaidInCapitalCommonStock" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RetainedEarningsAccumulatedDeficit"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StockholdersEquity" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockholdersEquity"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RetainedEarningsAccumulatedDeficit" xlink:to="us-gaap_StockholdersEquity" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesAndStockholdersEquity"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_LiabilitiesAndStockholdersEquity" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ConsolidatedBalanceSheet_Parentheticals" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfFinancialPositionAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfFinancialPositionAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_StatementTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_DebtInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentNameDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentNameDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="us-gaap_DebtInstrumentNameDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2026Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2026Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2026Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2030Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2030Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2030Member" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2028Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2028Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2028Member" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CommonStockParOrStatedValuePerShare" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockParOrStatedValuePerShare"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockParOrStatedValuePerShare" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CommonStockSharesAuthorized" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockSharesAuthorized"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockSharesAuthorized" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CommonStockSharesIssued" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockSharesIssued"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockSharesIssued" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CommonStockSharesOutstanding" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockSharesOutstanding"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockSharesOutstanding" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ConsolidatedIncomeStatement" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_IncomeStatementAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncomeStatementAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementAbstract" xlink:to="us-gaap_StatementTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_ProductOrServiceAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductOrServiceAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="srt_ProductOrServiceAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_ProductsAndServicesDomain" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductsAndServicesDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="srt_ProductsAndServicesDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ProductMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProductMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="us-gaap_ProductMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RoyaltyMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RoyaltyMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="us-gaap_RoyaltyMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="OtherCommercialMember" xlink:href="ions-20260630.xsd#ions_OtherCommercialMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="OtherCommercialMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CommercialMember" xlink:href="ions-20260630.xsd#ions_CommercialMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="CommercialMember" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CollaborativeAgreementRevenueMember" xlink:href="ions-20260630.xsd#ions_CollaborativeAgreementRevenueMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="CollaborativeAgreementRevenueMember" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="WainuaJointDevelopmentRevenueMember" xlink:href="ions-20260630.xsd#ions_WainuaJointDevelopmentRevenueMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="WainuaJointDevelopmentRevenueMember" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ResearchAndDevelopmentRevenueMember" xlink:href="ions-20260630.xsd#ions_ResearchAndDevelopmentRevenueMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="ResearchAndDevelopmentRevenueMember" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerAbstract" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CostsAndExpensesAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CostsAndExpensesAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CostsAndExpensesAbstract" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CostOfGoodsAndServicesSold" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CostOfGoodsAndServicesSold"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CostsAndExpensesAbstract" xlink:to="us-gaap_CostOfGoodsAndServicesSold" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ResearchDevelopmentAndPatentExpense" xlink:href="ions-20260630.xsd#ions_ResearchDevelopmentAndPatentExpense"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CostsAndExpensesAbstract" xlink:to="ResearchDevelopmentAndPatentExpense" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SellingGeneralAndAdministrativeExpense" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SellingGeneralAndAdministrativeExpense"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CostsAndExpensesAbstract" xlink:to="us-gaap_SellingGeneralAndAdministrativeExpense" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CostsAndExpenses" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CostsAndExpenses"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SellingGeneralAndAdministrativeExpense" xlink:to="us-gaap_CostsAndExpenses" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OperatingIncomeLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingIncomeLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SellingGeneralAndAdministrativeExpense" xlink:to="us-gaap_OperatingIncomeLoss" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NonoperatingIncomeExpenseAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NonoperatingIncomeExpenseAbstract" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InvestmentIncomeNet" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentIncomeNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_InvestmentIncomeNet" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InterestExpense" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InterestExpense"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_InterestExpense" order="1.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="InterestExpenseAndAmortizationOfIssuanceCostsRelatedToSaleOfFutureRoyalties" xlink:href="ions-20260630.xsd#ions_InterestExpenseAndAmortizationOfIssuanceCostsRelatedToSaleOfFutureRoyalties"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="InterestExpenseAndAmortizationOfIssuanceCostsRelatedToSaleOfFutureRoyalties" order="2.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_GainLossOnInvestments" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GainLossOnInvestments"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_GainLossOnInvestments" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherNonoperatingIncomeExpense" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherNonoperatingIncomeExpense"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_OtherNonoperatingIncomeExpense" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncomeTaxExpenseBenefit" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncomeTaxExpenseBenefit"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_IncomeTaxExpenseBenefit" order="4.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NetIncomeLoss" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareBasic" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareBasic"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_EarningsPerShareBasic" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareDiluted" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareDiluted"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_EarningsPerShareDiluted" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberOfSharesOutstandingBasic"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ConsolidatedComprehensiveIncome" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_NetIncomeLoss" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeForeignCurrencyTransactionAndTranslationGainLossArisingDuringPeriodNetOfTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherComprehensiveIncomeForeignCurrencyTransactionAndTranslationGainLossArisingDuringPeriodNetOfTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_OtherComprehensiveIncomeForeignCurrencyTransactionAndTranslationGainLossArisingDuringPeriodNetOfTax" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ComprehensiveIncomeNetOfTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ComprehensiveIncomeNetOfTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_ComprehensiveIncomeNetOfTax" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ShareholdersEquityType2or3" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfStockholdersEquityAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfStockholdersEquityAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfStockholdersEquityAbstract" xlink:to="us-gaap_StatementTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementEquityComponentsAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CommonStockMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_CommonStockMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AdditionalPaidInCapitalMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AdditionalPaidInCapitalMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_AdditionalPaidInCapitalMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RetainedEarningsMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RetainedEarningsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_RetainedEarningsMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquityComponentDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="4.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StockholdersEquity" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockholdersEquity"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockholdersEquity" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SharesIssued" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SharesIssued"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_SharesIssued" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NetIncomeLoss" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeForeignCurrencyTransactionAndTranslationGainLossArisingDuringPeriodNetOfTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherComprehensiveIncomeForeignCurrencyTransactionAndTranslationGainLossArisingDuringPeriodNetOfTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_OtherComprehensiveIncomeForeignCurrencyTransactionAndTranslationGainLossArisingDuringPeriodNetOfTax" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodValueShareBasedCompensationGross" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodValueShareBasedCompensationGross"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueShareBasedCompensationGross" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesShareBasedCompensation" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodSharesShareBasedCompensation"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesShareBasedCompensation" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodValueConversionOfConvertibleSecurities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodValueConversionOfConvertibleSecurities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueConversionOfConvertibleSecurities" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesConversionOfConvertibleSecurities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodSharesConversionOfConvertibleSecurities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesConversionOfConvertibleSecurities" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RetirementOfSharesReceivedFromExerciseOfBondHedgesValue" xlink:href="ions-20260630.xsd#ions_RetirementOfSharesReceivedFromExerciseOfBondHedgesValue"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="RetirementOfSharesReceivedFromExerciseOfBondHedgesValue" order="10.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RetirementOfSharesReceivedFromExerciseOfBondHedgesShares" xlink:href="ions-20260630.xsd#ions_RetirementOfSharesReceivedFromExerciseOfBondHedgesShares"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="RetirementOfSharesReceivedFromExerciseOfBondHedgesShares" order="11.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StockholdersEquity_0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockholdersEquity"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockholdersEquity_0" order="12.0" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SharesIssued_0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SharesIssued"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_SharesIssued_0" order="13.0" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ShareholdersEquityType2or3_Parentheticals" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfStockholdersEquityAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfStockholdersEquityAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfStockholdersEquityAbstract" xlink:to="us-gaap_StatementTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_DebtInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2026Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2026Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2026Member" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ConsolidatedCashFlow" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfCashFlowsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfCashFlowsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_NetIncomeLoss" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_Depreciation" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Depreciation"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_Depreciation" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OperatingLeaseRightOfUseAssetAmortizationExpense" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseRightOfUseAssetAmortizationExpense"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_OperatingLeaseRightOfUseAssetAmortizationExpense" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AmortizationOfIntangibleAssets" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AmortizationOfIntangibleAssets"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_AmortizationOfIntangibleAssets" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" order="3.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AmortizationOfFinancingCosts" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AmortizationOfFinancingCosts"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_AmortizationOfFinancingCosts" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RoyaltyPayments" xlink:href="ions-20260630.xsd#ions_RoyaltyPayments"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="RoyaltyPayments" order="5.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="InterestExpenseRelatedToSaleOfFutureRoyalties" xlink:href="ions-20260630.xsd#ions_InterestExpenseRelatedToSaleOfFutureRoyalties"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="InterestExpenseRelatedToSaleOfFutureRoyalties" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensation" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensation"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_ShareBasedCompensation" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RealizedInvestmentGainsLosses" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RealizedInvestmentGainsLosses"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_RealizedInvestmentGainsLosses" order="8.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ImpairmentOfIntangibleAssetsFinitelived" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ImpairmentOfIntangibleAssetsFinitelived"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_ImpairmentOfIntangibleAssetsFinitelived" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInOperatingCapitalAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInContractWithCustomerAsset" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInContractWithCustomerAsset"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInContractWithCustomerAsset" order="0.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInInventories" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInInventories"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInInventories" order="1.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInOtherOperatingAssets" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInOtherOperatingAssets"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInOtherOperatingAssets" order="2.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInAccountsPayable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInAccountsPayable" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInAccruedIncomeTaxesPayable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInAccruedIncomeTaxesPayable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInAccruedIncomeTaxesPayable" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInOtherEmployeeRelatedLiabilities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInOtherEmployeeRelatedLiabilities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInOtherEmployeeRelatedLiabilities" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInOtherCurrentLiabilities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInOtherCurrentLiabilities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInOtherCurrentLiabilities" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInContractWithCustomerLiability" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInContractWithCustomerLiability"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInContractWithCustomerLiability" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivities" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt" order="0.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ProceedsFromSaleAndMaturityOfAvailableForSaleSecurities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProceedsFromSaleAndMaturityOfAvailableForSaleSecurities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromSaleAndMaturityOfAvailableForSaleSecurities" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" order="2.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_PaymentsToAcquireIntangibleAssets" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsToAcquireIntangibleAssets"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_PaymentsToAcquireIntangibleAssets" order="3.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PaymentsToAcquireIntangibleAssets" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivities" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ProceedsFromIssuanceOfSharesUnderIncentiveAndShareBasedCompensationPlansIncludingStockOptions" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProceedsFromIssuanceOfSharesUnderIncentiveAndShareBasedCompensationPlansIncludingStockOptions"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromIssuanceOfSharesUnderIncentiveAndShareBasedCompensationPlansIncludingStockOptions" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RepaymentsOfConvertibleDebt" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RepaymentsOfConvertibleDebt"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_RepaymentsOfConvertibleDebt" order="1.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RepaymentsOfSecuredDebt" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RepaymentsOfSecuredDebt"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_RepaymentsOfSecuredDebt" order="2.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RepaymentsOfSecuredDebt" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivities" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents_0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents_0" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SupplementalCashFlowInformationAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SupplementalCashFlowInformationAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_SupplementalCashFlowInformationAbstract" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InterestPaidNet" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InterestPaidNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SupplementalCashFlowInformationAbstract" xlink:to="us-gaap_InterestPaidNet" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncomeTaxesPaidNet" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncomeTaxesPaidNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SupplementalCashFlowInformationAbstract" xlink:to="us-gaap_IncomeTaxesPaidNet" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CashFlowNoncashInvestingAndFinancingActivitiesDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashFlowNoncashInvestingAndFinancingActivitiesDisclosureAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_CashFlowNoncashInvestingAndFinancingActivitiesDisclosureAbstract" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RightOfUseAssetObtainedInExchangeForOperatingLeaseLiability" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RightOfUseAssetObtainedInExchangeForOperatingLeaseLiability"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CashFlowNoncashInvestingAndFinancingActivitiesDisclosureAbstract" xlink:to="us-gaap_RightOfUseAssetObtainedInExchangeForOperatingLeaseLiability" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CapitalAndPatentExpendituresIncurredButNotYetPaid" xlink:href="ions-20260630.xsd#ions_CapitalAndPatentExpendituresIncurredButNotYetPaid"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CashFlowNoncashInvestingAndFinancingActivitiesDisclosureAbstract" xlink:to="CapitalAndPatentExpendituresIncurredButNotYetPaid" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ConsolidatedCashFlow_Parentheticals" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfCashFlowsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfCashFlowsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_StatementTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_DebtInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2026Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2026Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2026Member" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/OrganizationandBasisofPresentation" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/SignificantAccountingPolicies" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccountingPoliciesAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SignificantAccountingPoliciesTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SignificantAccountingPoliciesTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_SignificantAccountingPoliciesTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/SupplementalFinancialData" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="SupplementalFinancialDataAbstract" xlink:href="ions-20260630.xsd#ions_SupplementalFinancialDataAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SupplementalBalanceSheetDisclosuresTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SupplementalBalanceSheetDisclosuresTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SupplementalFinancialDataAbstract" xlink:to="us-gaap_SupplementalBalanceSheetDisclosuresTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/Revenues" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:to="us-gaap_RevenueFromContractWithCustomerTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreements" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementDisclosureTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementDisclosureTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_CollaborativeArrangementDisclosureTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/BasicandDilutedNetIncomeLossPerShare" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareAbstract"/>
    <loc xlink:type="locator" xlink:label="BasicandDilutedNetIncomeLossPerShareTable" xlink:href="ions-20260630.xsd#ions_BasicandDilutedNetIncomeLossPerShareTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="BasicandDilutedNetIncomeLossPerShareTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="BasicandDilutedNetIncomeLossPerShareLineItems" xlink:href="ions-20260630.xsd#ions_BasicandDilutedNetIncomeLossPerShareLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BasicandDilutedNetIncomeLossPerShareTable" xlink:to="BasicandDilutedNetIncomeLossPerShareLineItems" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BasicandDilutedNetIncomeLossPerShareLineItems" xlink:to="us-gaap_EarningsPerShareTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/Investments" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_InvestmentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InvestmentTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="us-gaap_InvestmentTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/FairValueMeasurements" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueDisclosuresAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueDisclosuresTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_FairValueDisclosuresTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/StockbasedCompensationExpense" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/LiabilityRelatedtoSaleofFutureRoyalties" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherLiabilitiesDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="LiabilityRelatedtoSaleofFutureRoyaltiesTable" xlink:href="ions-20260630.xsd#ions_LiabilityRelatedtoSaleofFutureRoyaltiesTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherLiabilitiesDisclosureAbstract" xlink:to="LiabilityRelatedtoSaleofFutureRoyaltiesTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="LiabilityRelatedtoSaleofFutureRoyaltiesLineItems" xlink:href="ions-20260630.xsd#ions_LiabilityRelatedtoSaleofFutureRoyaltiesLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="LiabilityRelatedtoSaleofFutureRoyaltiesTable" xlink:to="LiabilityRelatedtoSaleofFutureRoyaltiesLineItems" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesDisclosureTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherLiabilitiesDisclosureTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="LiabilityRelatedtoSaleofFutureRoyaltiesLineItems" xlink:to="us-gaap_OtherLiabilitiesDisclosureTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ConvertibleDebt" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DebtDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtDisclosureTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtDisclosureTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_DebtDisclosureTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/LegalProceedings" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_LegalMattersAndContingenciesTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LegalMattersAndContingenciesTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_LegalMattersAndContingenciesTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/SegmentInformation" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_SegmentReportingAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SegmentReportingDisclosureTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingDisclosureTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingAbstract" xlink:to="us-gaap_SegmentReportingDisclosureTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/AccountingPoliciesByPolicy" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccountingPoliciesAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_BasisOfAccountingPolicyPolicyTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_BasisOfAccountingPolicyPolicyTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_BasisOfAccountingPolicyPolicyTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConsolidationPolicyTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConsolidationPolicyTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_ConsolidationPolicyTextBlock" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SegmentReportingPolicyPolicyTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingPolicyPolicyTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_SegmentReportingPolicyPolicyTextBlock" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_UseOfEstimates" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_UseOfEstimates"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_UseOfEstimates" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NewAccountingPronouncementsPolicyPolicyTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NewAccountingPronouncementsPolicyPolicyTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_NewAccountingPronouncementsPolicyPolicyTextBlock" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerSharePolicyTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerSharePolicyTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_EarningsPerSharePolicyTextBlock" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/SupplementalFinancialDataTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="SupplementalFinancialDataAbstract" xlink:href="ions-20260630.xsd#ions_SupplementalFinancialDataAbstract"/>
    <loc xlink:type="locator" xlink:label="ScheduleOfInventoryCurrentAndNoncurrentTableTextBlock" xlink:href="ions-20260630.xsd#ions_ScheduleOfInventoryCurrentAndNoncurrentTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SupplementalFinancialDataAbstract" xlink:to="ScheduleOfInventoryCurrentAndNoncurrentTableTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfAccruedLiabilitiesTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfAccruedLiabilitiesTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SupplementalFinancialDataAbstract" xlink:to="us-gaap_ScheduleOfAccruedLiabilitiesTableTextBlock" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/RevenuesTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DisaggregationOfRevenueTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:to="us-gaap_DisaggregationOfRevenueTableTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="BiogenCollaborationsMember" xlink:href="ions-20260630.xsd#ions_BiogenCollaborationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="BiogenCollaborationsMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="GlaxoSmithKlineCollaborationMember" xlink:href="ions-20260630.xsd#ions_GlaxoSmithKlineCollaborationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="GlaxoSmithKlineCollaborationMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="OnoCollaborationMember" xlink:href="ions-20260630.xsd#ions_OnoCollaborationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="OnoCollaborationMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="OtsukaCollaborationsMember" xlink:href="ions-20260630.xsd#ions_OtsukaCollaborationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="OtsukaCollaborationsMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RecordatiAgCollaborationMember" xlink:href="ions-20260630.xsd#ions_RecordatiAgCollaborationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RecordatiAgCollaborationMember" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RocheCollaborationsMember" xlink:href="ions-20260630.xsd#ions_RocheCollaborationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RocheCollaborationsMember" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SchedulesOfConcentrationOfRiskByRiskFactorTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SchedulesOfConcentrationOfRiskByRiskFactorTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_SchedulesOfConcentrationOfRiskByRiskFactorTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/BasicandDilutedNetIncomeLossPerShareTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareAbstract"/>
    <loc xlink:type="locator" xlink:label="BasicandDilutedNetIncomeLossPerShareTablesTable" xlink:href="ions-20260630.xsd#ions_BasicandDilutedNetIncomeLossPerShareTablesTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="BasicandDilutedNetIncomeLossPerShareTablesTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="BasicandDilutedNetIncomeLossPerShareTablesLineItems" xlink:href="ions-20260630.xsd#ions_BasicandDilutedNetIncomeLossPerShareTablesLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BasicandDilutedNetIncomeLossPerShareTablesTable" xlink:to="BasicandDilutedNetIncomeLossPerShareTablesLineItems" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfEarningsPerShareBasicAndDilutedTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfEarningsPerShareBasicAndDilutedTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BasicandDilutedNetIncomeLossPerShareTablesLineItems" xlink:to="us-gaap_ScheduleOfEarningsPerShareBasicAndDilutedTableTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/InvestmentsTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_InvestmentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InvestmentsClassifiedByContractualMaturityDateTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentsClassifiedByContractualMaturityDateTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="us-gaap_InvestmentsClassifiedByContractualMaturityDateTableTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_UnrealizedGainLossOnInvestmentsTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_UnrealizedGainLossOnInvestmentsTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="us-gaap_UnrealizedGainLossOnInvestmentsTableTextBlock" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionFairValueTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionFairValueTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionFairValueTableTextBlock" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/FairValueMeasurementsTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueDisclosuresAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueAssetsMeasuredOnRecurringBasisTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsMeasuredOnRecurringBasisTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_FairValueAssetsMeasuredOnRecurringBasisTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/StockbasedCompensationExpenseTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedPaymentAwardStockOptionsValuationAssumptionsTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfShareBasedPaymentAwardStockOptionsValuationAssumptionsTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfShareBasedPaymentAwardStockOptionsValuationAssumptionsTableTextBlock" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedPaymentAwardEmployeeStockPurchasePlanValuationAssumptionsTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfShareBasedPaymentAwardEmployeeStockPurchasePlanValuationAssumptionsTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfShareBasedPaymentAwardEmployeeStockPurchasePlanValuationAssumptionsTableTextBlock" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/LiabilityRelatedtoSaleofFutureRoyaltiesTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherLiabilitiesDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherNoncurrentLiabilitiesTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherNoncurrentLiabilitiesTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherLiabilitiesDisclosureAbstract" xlink:to="us-gaap_OtherNoncurrentLiabilitiesTableTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ConvertibleDebtTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DebtDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="ConvertibleNotesDisclosureTable" xlink:href="ions-20260630.xsd#ions_ConvertibleNotesDisclosureTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="ConvertibleNotesDisclosureTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ConvertibleNotesDisclosureTable" xlink:to="us-gaap_DebtInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2030Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2030Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2030Member" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2028Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2028Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2028Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ConvertibleNotesDisclosureTable" xlink:to="us-gaap_DebtInstrumentLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConvertibleDebtTableTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConvertibleDebtTableTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_ConvertibleDebtTableTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/SegmentInformationTables" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_SegmentReportingAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfSegmentReportingInformationBySegmentTextBlock" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfSegmentReportingInformationBySegmentTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingAbstract" xlink:to="us-gaap_ScheduleOfSegmentReportingInformationBySegmentTextBlock" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/InventoriesTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_InventoryNetAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InventoryNetAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InventoryCurrentTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InventoryCurrentTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InventoryNetAbstract" xlink:to="us-gaap_InventoryCurrentTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfFinancialPositionLocationBalanceAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfFinancialPositionLocationBalanceAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InventoryCurrentTable" xlink:to="us-gaap_StatementOfFinancialPositionLocationBalanceAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InventoryLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InventoryLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InventoryCurrentTable" xlink:to="us-gaap_InventoryLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="InventoryRawMaterialsNet" xlink:href="ions-20260630.xsd#ions_InventoryRawMaterialsNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InventoryLineItems" xlink:to="InventoryRawMaterialsNet" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="InventoryWorkInProcessNet" xlink:href="ions-20260630.xsd#ions_InventoryWorkInProcessNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InventoryLineItems" xlink:to="InventoryWorkInProcessNet" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="InventoryFinishedGoodsNet" xlink:href="ions-20260630.xsd#ions_InventoryFinishedGoodsNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InventoryLineItems" xlink:to="InventoryFinishedGoodsNet" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="InventoryCurrentAndNoncurrent" xlink:href="ions-20260630.xsd#ions_InventoryCurrentAndNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="InventoryFinishedGoodsNet" xlink:to="InventoryCurrentAndNoncurrent" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InventoryAdjustmentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InventoryAdjustmentsAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InventoryLineItems" xlink:to="us-gaap_InventoryAdjustmentsAbstract" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InventoryNet" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InventoryNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InventoryAdjustmentsAbstract" xlink:to="us-gaap_InventoryNet" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_InventoryNoncurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InventoryNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InventoryAdjustmentsAbstract" xlink:to="us-gaap_InventoryNoncurrent" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/AccruedLiabilitiesTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_AccruedLiabilitiesCurrentAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccruedLiabilitiesCurrentAbstract"/>
    <loc xlink:type="locator" xlink:label="AccruedClinicalExpenses" xlink:href="ions-20260630.xsd#ions_AccruedClinicalExpenses"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccruedLiabilitiesCurrentAbstract" xlink:to="AccruedClinicalExpenses" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="AccruedInLicensingFeesCurrent" xlink:href="ions-20260630.xsd#ions_AccruedInLicensingFeesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccruedLiabilitiesCurrentAbstract" xlink:to="AccruedInLicensingFeesCurrent" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="AccruedCommercialExpensesCurrent" xlink:href="ions-20260630.xsd#ions_AccruedCommercialExpensesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccruedLiabilitiesCurrentAbstract" xlink:to="AccruedCommercialExpensesCurrent" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherAccruedLiabilitiesCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherAccruedLiabilitiesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccruedLiabilitiesCurrentAbstract" xlink:to="us-gaap_OtherAccruedLiabilitiesCurrent" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AccruedLiabilitiesCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccruedLiabilitiesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccruedLiabilitiesCurrentAbstract" xlink:to="us-gaap_AccruedLiabilitiesCurrent" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/RevenuesTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DisaggregationOfRevenueTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:to="us-gaap_DisaggregationOfRevenueTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_ProductOrServiceAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductOrServiceAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueTable" xlink:to="srt_ProductOrServiceAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_ProductsAndServicesDomain" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductsAndServicesDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="srt_ProductsAndServicesDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="TryngolzaMember" xlink:href="ions-20260630.xsd#ions_TryngolzaMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="TryngolzaMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="DAWNZERASalesMember" xlink:href="ions-20260630.xsd#ions_DAWNZERASalesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="DAWNZERASalesMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ProductMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProductMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="us-gaap_ProductMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="SpinrazaRoyaltiesMember" xlink:href="ions-20260630.xsd#ions_SpinrazaRoyaltiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="SpinrazaRoyaltiesMember" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="WainusRoyaltiesMember" xlink:href="ions-20260630.xsd#ions_WainusRoyaltiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="WainusRoyaltiesMember" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="OtherRoyaltiesMember" xlink:href="ions-20260630.xsd#ions_OtherRoyaltiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="OtherRoyaltiesMember" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RoyaltyMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RoyaltyMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="us-gaap_RoyaltyMember" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="OtherCommercialMember" xlink:href="ions-20260630.xsd#ions_OtherCommercialMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="OtherCommercialMember" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CommercialMember" xlink:href="ions-20260630.xsd#ions_CommercialMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="CommercialMember" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CollaborativeAgreementRevenueMember" xlink:href="ions-20260630.xsd#ions_CollaborativeAgreementRevenueMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="CollaborativeAgreementRevenueMember" order="10.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="WainuaJointDevelopmentRevenueMember" xlink:href="ions-20260630.xsd#ions_WainuaJointDevelopmentRevenueMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="WainuaJointDevelopmentRevenueMember" order="11.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ResearchAndDevelopmentRevenueMember" xlink:href="ions-20260630.xsd#ions_ResearchAndDevelopmentRevenueMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="ResearchAndDevelopmentRevenueMember" order="12.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DisaggregationOfRevenueLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueTable" xlink:to="us-gaap_DisaggregationOfRevenueLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DisaggregationOfRevenueAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueLineItems" xlink:to="us-gaap_DisaggregationOfRevenueAbstract" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueAbstract" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithBiogenTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="BiogenCollaborationsMember" xlink:href="ions-20260630.xsd#ions_BiogenCollaborationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="BiogenCollaborationsMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByBenchmarkAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskBenchmarkDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_ConcentrationRiskBenchmarkDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_RevenueFromContractWithCustomerMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByTypeAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskTypeDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_ConcentrationRiskTypeDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CustomerConcentrationRiskMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CustomerConcentrationRiskMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_CustomerConcentrationRiskMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskPercentage1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskPercentage1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ConcentrationRiskPercentage1" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithGSKTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="GlaxoSmithKlineCollaborationMember" xlink:href="ions-20260630.xsd#ions_GlaxoSmithKlineCollaborationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="GlaxoSmithKlineCollaborationMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByBenchmarkAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskBenchmarkDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_ConcentrationRiskBenchmarkDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_RevenueFromContractWithCustomerMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByTypeAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskTypeDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_ConcentrationRiskTypeDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CustomerConcentrationRiskMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CustomerConcentrationRiskMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_CustomerConcentrationRiskMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskPercentage1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskPercentage1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ConcentrationRiskPercentage1" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithOnoTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="OnoCollaborationMember" xlink:href="ions-20260630.xsd#ions_OnoCollaborationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="OnoCollaborationMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByBenchmarkAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskBenchmarkDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_ConcentrationRiskBenchmarkDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_RevenueFromContractWithCustomerMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByTypeAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskTypeDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_ConcentrationRiskTypeDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CustomerConcentrationRiskMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CustomerConcentrationRiskMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_CustomerConcentrationRiskMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskPercentage1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskPercentage1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ConcentrationRiskPercentage1" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithOtsukaTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="OtsukaCollaborationsMember" xlink:href="ions-20260630.xsd#ions_OtsukaCollaborationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="OtsukaCollaborationsMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByBenchmarkAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskBenchmarkDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_ConcentrationRiskBenchmarkDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_RevenueFromContractWithCustomerMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByTypeAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskTypeDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_ConcentrationRiskTypeDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CustomerConcentrationRiskMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CustomerConcentrationRiskMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_CustomerConcentrationRiskMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskPercentage1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskPercentage1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ConcentrationRiskPercentage1" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithRecordatiTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="RecordatiAgCollaborationMember" xlink:href="ions-20260630.xsd#ions_RecordatiAgCollaborationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RecordatiAgCollaborationMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByBenchmarkAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskBenchmarkDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_ConcentrationRiskBenchmarkDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_RevenueFromContractWithCustomerMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByTypeAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskTypeDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_ConcentrationRiskTypeDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CustomerConcentrationRiskMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CustomerConcentrationRiskMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_CustomerConcentrationRiskMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskPercentage1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskPercentage1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ConcentrationRiskPercentage1" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/RevenuefromCollaborativeRelationshipwithRocheTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="RocheCollaborationsMember" xlink:href="ions-20260630.xsd#ions_RocheCollaborationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RocheCollaborationsMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByBenchmarkAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskBenchmarkDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_ConcentrationRiskBenchmarkDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByBenchmarkAxis" xlink:to="us-gaap_RevenueFromContractWithCustomerMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskByTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_ConcentrationRiskByTypeAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskTypeDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_ConcentrationRiskTypeDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CustomerConcentrationRiskMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CustomerConcentrationRiskMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ConcentrationRiskByTypeAxis" xlink:to="us-gaap_CustomerConcentrationRiskMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ConcentrationRiskPercentage1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskPercentage1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ConcentrationRiskPercentage1" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/DilutedNetIncomePerShareTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AntidilutiveSecuritiesNameDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeStockOptionMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockOptionMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_EmployeeStockOptionMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RestrictedStockUnitsRSUMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RestrictedStockUnitsRSUMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_RestrictedStockUnitsRSUMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="us-gaap_DebtInstrumentAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentNameDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentNameDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="us-gaap_DebtInstrumentNameDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2028Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2028Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2028Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2026Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2026Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2026Member" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareBasicLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareBasicLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="us-gaap_EarningsPerShareBasicLineItems" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberOfSharesOutstandingBasic"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareBasic" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareBasic"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_EarningsPerShareBasic" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustmentAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustmentAbstract"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustmentAbstract" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncrementalCommonSharesAttributableToShareBasedPaymentArrangements" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncrementalCommonSharesAttributableToShareBasedPaymentArrangements"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustmentAbstract" xlink:to="us-gaap_IncrementalCommonSharesAttributableToShareBasedPaymentArrangements" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="SharesIssuableRelatedToEmployeeStockPurchasePlan" xlink:href="ions-20260630.xsd#ions_SharesIssuableRelatedToEmployeeStockPurchasePlan"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustmentAbstract" xlink:to="SharesIssuableRelatedToEmployeeStockPurchasePlan" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DilutiveSecuritiesEffectOnBasicEarningsPerShareOther" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DilutiveSecuritiesEffectOnBasicEarningsPerShareOther"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustmentAbstract" xlink:to="us-gaap_DilutiveSecuritiesEffectOnBasicEarningsPerShareOther" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_IncrementalCommonSharesAttributableToConversionOfDebtSecurities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncrementalCommonSharesAttributableToConversionOfDebtSecurities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustmentAbstract" xlink:to="us-gaap_IncrementalCommonSharesAttributableToConversionOfDebtSecurities" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustmentAbstract" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage_0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_NetIncomeLossAvailableToCommonStockholdersDiluted" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareDiluted" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareDiluted"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_EarningsPerShareDiluted" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ContractMaturityofAvailableforSaleSecuritiesTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_InvestmentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentsAbstract"/>
    <loc xlink:type="locator" xlink:label="AvailableForSaleSecuritiesDebtMaturitiesWithinOneYearPercentage" xlink:href="ions-20260630.xsd#ions_AvailableForSaleSecuritiesDebtMaturitiesWithinOneYearPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="AvailableForSaleSecuritiesDebtMaturitiesWithinOneYearPercentage" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumContractMaturityPeriodRange1" xlink:href="ions-20260630.xsd#ions_MaximumContractMaturityPeriodRange1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="MaximumContractMaturityPeriodRange1" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="AvailableForSaleSecuritiesDebtMaturitiesAfterOneThroughTwoYearsPercentage" xlink:href="ions-20260630.xsd#ions_AvailableForSaleSecuritiesDebtMaturitiesAfterOneThroughTwoYearsPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="AvailableForSaleSecuritiesDebtMaturitiesAfterOneThroughTwoYearsPercentage" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumContractMaturityPeriodRange1_0" xlink:href="ions-20260630.xsd#ions_MaximumContractMaturityPeriodRange1"/>
    <loc xlink:type="locator" xlink:label="MaximumContractMaturityPeriodRange2" xlink:href="ions-20260630.xsd#ions_MaximumContractMaturityPeriodRange2"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="MaximumContractMaturityPeriodRange2" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="AvailableForSaleSecuritiesDebtMaturitiesAfterTwoThroughThreeAndOneHalfYearsPercentage" xlink:href="ions-20260630.xsd#ions_AvailableForSaleSecuritiesDebtMaturitiesAfterTwoThroughThreeAndOneHalfYearsPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="AvailableForSaleSecuritiesDebtMaturitiesAfterTwoThroughThreeAndOneHalfYearsPercentage" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumContractMaturityPeriodRange2_0" xlink:href="ions-20260630.xsd#ions_MaximumContractMaturityPeriodRange2"/>
    <loc xlink:type="locator" xlink:label="MaximumContractMaturityPeriodRange3" xlink:href="ions-20260630.xsd#ions_MaximumContractMaturityPeriodRange3"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="MaximumContractMaturityPeriodRange3" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="AvailableForSaleSecuritiesDebtMaturitiesTotalPercentage" xlink:href="ions-20260630.xsd#ions_AvailableForSaleSecuritiesDebtMaturitiesTotalPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="AvailableForSaleSecuritiesDebtMaturitiesTotalPercentage" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/SummaryofInvestmentsTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_InvestmentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FinancialInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinancialInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable" xlink:to="us-gaap_FinancialInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CorporateDebtSecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CorporateDebtSecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_CorporateDebtSecuritiesMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USGovernmentAgenciesDebtSecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_USTreasurySecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USTreasurySecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_USTreasurySecuritiesMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_USStatesAndPoliticalSubdivisionsMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USStatesAndPoliticalSubdivisionsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_USStatesAndPoliticalSubdivisionsMember" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="EquitySecuritiesPubliclyTradedCompaniesMember" xlink:href="ions-20260630.xsd#ions_EquitySecuritiesPubliclyTradedCompaniesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="EquitySecuritiesPubliclyTradedCompaniesMember" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="EquitySecuritiesPrivateCompaniesMember" xlink:href="ions-20260630.xsd#ions_EquitySecuritiesPrivateCompaniesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="EquitySecuritiesPrivateCompaniesMember" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_OtherDebtSecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherDebtSecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_OtherDebtSecuritiesMember" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="EquitySecuritiesPrivatelyHeldInvesteeThatBecamePubliclyTradedEntityMember" xlink:href="ions-20260630.xsd#ions_EquitySecuritiesPrivatelyHeldInvesteeThatBecamePubliclyTradedEntityMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="EquitySecuritiesPrivatelyHeldInvesteeThatBecamePubliclyTradedEntityMember" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable" xlink:to="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleAmortizedCostCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleAmortizedCostCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleAmortizedCostCurrent" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedGainBeforeTaxCurrent" xlink:href="ions-20260630.xsd#ions_DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedGainBeforeTaxCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedGainBeforeTaxCurrent" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedLossBeforeTaxCurrent" xlink:href="ions-20260630.xsd#ions_DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedLossBeforeTaxCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedLossBeforeTaxCurrent" order="2.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleAmortizedCostNoncurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleAmortizedCostNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleAmortizedCostNoncurrent" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedGainBeforeTaxNoncurrent" xlink:href="ions-20260630.xsd#ions_DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedGainBeforeTaxNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedGainBeforeTaxNoncurrent" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedLossBeforeTaxNoncurrent" xlink:href="ions-20260630.xsd#ions_DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedLossBeforeTaxNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="DebtSecuritiesAvailableForSaleAccumulatedGrossUnrealizedLossBeforeTaxNoncurrent" order="6.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" order="10.0" preferredLabel="http://www.xbrl.org/2009/role/negatedTotalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecurities" order="11.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EquitySecuritiesFvNiCost" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquitySecuritiesFvNiCost"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_EquitySecuritiesFvNiCost" order="12.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="EquitySecuritiesFvNiAccumulatedGrossUnrealizedGain" xlink:href="ions-20260630.xsd#ions_EquitySecuritiesFvNiAccumulatedGrossUnrealizedGain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="EquitySecuritiesFvNiAccumulatedGrossUnrealizedGain" order="13.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="EquitySecuritiesFvNiAccumulatedGrossUnrealizedLoss" xlink:href="ions-20260630.xsd#ions_EquitySecuritiesFvNiAccumulatedGrossUnrealizedLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="EquitySecuritiesFvNiAccumulatedGrossUnrealizedLoss" order="14.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EquitySecuritiesFvNi" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquitySecuritiesFvNi"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_EquitySecuritiesFvNi" order="15.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNiCost" xlink:href="ions-20260630.xsd#ions_DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNiCost"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNiCost" order="16.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNiGrossUnrealizedGain" xlink:href="ions-20260630.xsd#ions_DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNiGrossUnrealizedGain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNiGrossUnrealizedGain" order="17.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNiGrossUnrealizedLoss" xlink:href="ions-20260630.xsd#ions_DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNiGrossUnrealizedLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNiGrossUnrealizedLoss" order="18.0" preferredLabel="http://www.xbrl.org/2009/role/negatedTotalLabel"/>
    <loc xlink:type="locator" xlink:label="DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNi" xlink:href="ions-20260630.xsd#ions_DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNi"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="DebtSecuritiesAvailableForSaleAndEquitySecuritiesFvNi" order="19.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EquitySecuritiesFvNiUnrealizedGain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquitySecuritiesFvNiUnrealizedGain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_EquitySecuritiesFvNiUnrealizedGain" order="20.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EquitySecuritiesFvNiUnrealizedLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquitySecuritiesFvNiUnrealizedLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="us-gaap_EquitySecuritiesFvNiUnrealizedLoss" order="21.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EquitySecuritiesFvNi_0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquitySecuritiesFvNi"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EquitySecuritiesFvNiUnrealizedLoss_0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquitySecuritiesFvNiUnrealizedLoss"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EquitySecuritiesFvNi_1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquitySecuritiesFvNi"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/TemporarilyImpairedInvestmentsTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_InvestmentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FinancialInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinancialInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_FinancialInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CorporateDebtSecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CorporateDebtSecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_CorporateDebtSecuritiesMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USGovernmentAgenciesDebtSecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_USTreasurySecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USTreasurySecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_USTreasurySecuritiesMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_USStatesAndPoliticalSubdivisionsMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USStatesAndPoliticalSubdivisionsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_USStatesAndPoliticalSubdivisionsMember" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPositionLessThan12MonthsNumberOfPositions" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPositionLessThan12MonthsNumberOfPositions"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPositionLessThan12MonthsNumberOfPositions" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPositionLessThan12Months" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPositionLessThan12Months"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPositionLessThan12Months" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPositionLessThan12MonthsAccumulatedLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPositionLessThan12MonthsAccumulatedLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPositionLessThan12MonthsAccumulatedLoss" order="2.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLonger" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLonger"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLonger" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLongerAccumulatedLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLongerAccumulatedLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLongerAccumulatedLoss" order="4.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPosition" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPosition"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPosition" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionAccumulatedLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionAccumulatedLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionAccumulatedLoss" order="6.0" preferredLabel="http://www.xbrl.org/2009/role/negatedTotalLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/AssetsMeasuredatFairValueonaRecurringBasisTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueDisclosuresAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueByMeasurementFrequencyAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByMeasurementFrequencyAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsRecurringMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueMeasurementsRecurringMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementsRecurringMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByFairValueHierarchyLevelAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel1Member" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueInputsLevel1Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueInputsLevel1Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel2Member" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueInputsLevel2Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueInputsLevel2Member" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FinancialInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinancialInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FinancialInstrumentAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CorporateDebtSecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CorporateDebtSecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_CorporateDebtSecuritiesMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USGovernmentAgenciesDebtSecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_USTreasurySecuritiesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USTreasurySecuritiesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_USTreasurySecuritiesMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_USStatesAndPoliticalSubdivisionsMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USStatesAndPoliticalSubdivisionsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_USStatesAndPoliticalSubdivisionsMember" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="EquitySecuritiesPubliclyTradedCompaniesMember" xlink:href="ions-20260630.xsd#ions_EquitySecuritiesPubliclyTradedCompaniesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="EquitySecuritiesPubliclyTradedCompaniesMember" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfFinancialPositionLocationBalanceAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfFinancialPositionLocationBalanceAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_StatementOfFinancialPositionLocationBalanceAxis" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecurities" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EquitySecuritiesFvNi" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquitySecuritiesFvNi"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_EquitySecuritiesFvNi" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AssetsFairValueDisclosure" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AssetsFairValueDisclosure"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_AssetsFairValueDisclosure" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities_0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities_1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities_2" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/StockbasedCompensationExpenseTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementOfIncomeLocationBalanceAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfIncomeLocationBalanceAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:to="us-gaap_StatementOfIncomeLocationBalanceAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AllocatedShareBasedCompensationExpense"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsCapitalizedAmount" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsCapitalizedAmount"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsCapitalizedAmount" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardCompensationCost1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardCompensationCost1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardCompensationCost1" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/WeightedAverageAssumptionsforStockOptionsTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AwardTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AwardTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeStockOptionMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockOptionMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_EmployeeStockOptionMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_GranteeStatusAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GranteeStatusAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_GranteeStatusAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedPaymentArrangementEmployeeMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedPaymentArrangementEmployeeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GranteeStatusAxis" xlink:to="us-gaap_ShareBasedPaymentArrangementEmployeeMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedPaymentArrangementNonemployeeMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedPaymentArrangementNonemployeeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GranteeStatusAxis" xlink:to="us-gaap_ShareBasedPaymentArrangementNonemployeeMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsWeightedAverageVolatilityRate" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsWeightedAverageVolatilityRate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsWeightedAverageVolatilityRate" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/WeightedAverageAssumptionsforESPPTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AwardTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AwardTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeStockMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_EmployeeStockMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsWeightedAverageVolatilityRate" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsWeightedAverageVolatilityRate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsWeightedAverageVolatilityRate" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/LiabilityRelatedtoSaleofFutureRoyaltiesTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherLiabilitiesDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherLiabilitiesDisclosureAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="RoyaltyPurchaseAgreementMember" xlink:href="ions-20260630.xsd#ions_RoyaltyPurchaseAgreementMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RoyaltyPurchaseAgreementMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="LiabilityRelatedToSaleOfFutureRoyaltiesNet" xlink:href="ions-20260630.xsd#ions_LiabilityRelatedToSaleOfFutureRoyaltiesNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="LiabilityRelatedToSaleOfFutureRoyaltiesNet" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel"/>
    <loc xlink:type="locator" xlink:label="RoyaltyPayments" xlink:href="ions-20260630.xsd#ions_RoyaltyPayments"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="RoyaltyPayments" order="1.0" preferredLabel="http://www.xbrl.org/2009/role/negatedTerseLabel"/>
    <loc xlink:type="locator" xlink:label="InterestExpenseRelatedToSaleOfFutureRoyalties" xlink:href="ions-20260630.xsd#ions_InterestExpenseRelatedToSaleOfFutureRoyalties"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="InterestExpenseRelatedToSaleOfFutureRoyalties" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="AmortizationOfIssuanceCostsRelatedToSaleOfFutureRoyalties" xlink:href="ions-20260630.xsd#ions_AmortizationOfIssuanceCostsRelatedToSaleOfFutureRoyalties"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="AmortizationOfIssuanceCostsRelatedToSaleOfFutureRoyalties" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="LiabilityRelatedToSaleOfFutureRoyaltiesNet_0" xlink:href="ions-20260630.xsd#ions_LiabilityRelatedToSaleOfFutureRoyaltiesNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="LiabilityRelatedToSaleOfFutureRoyaltiesNet_0" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel"/>
    <loc xlink:type="locator" xlink:label="LiabilityRelatedToSaleOfFutureRoyaltiesNetCurrent" xlink:href="ions-20260630.xsd#ions_LiabilityRelatedToSaleOfFutureRoyaltiesNetCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="LiabilityRelatedToSaleOfFutureRoyaltiesNetCurrent" order="5.0" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
    <loc xlink:type="locator" xlink:label="LiabilityRelatedToSaleOfFutureRoyaltiesNetNoncurrent" xlink:href="ions-20260630.xsd#ions_LiabilityRelatedToSaleOfFutureRoyaltiesNetNoncurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="LiabilityRelatedToSaleOfFutureRoyaltiesNetNoncurrent" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/0Notesdue2030Table" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DebtDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_DebtInstrumentTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_DebtInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2030Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2030Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2030Member" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_DebtInstrumentLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentCarryingAmount" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentCarryingAmount"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentCarryingAmount" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DeferredFinanceCostsNet" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DeferredFinanceCostsNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DeferredFinanceCostsNet" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentMaturityDate" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentMaturityDate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentMaturityDate" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateEffectivePercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateEffectivePercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateEffectivePercentage" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentConvertibleConversionPrice1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentConvertibleConversionPrice1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentConvertibleConversionPrice1" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="DebtInstrumentConvertibleSharesSubjectToConversion" xlink:href="ions-20260630.xsd#ions_DebtInstrumentConvertibleSharesSubjectToConversion"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="DebtInstrumentConvertibleSharesSubjectToConversion" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage_0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/175Notesdue2028Table" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DebtDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_DebtInstrumentTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_DebtInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2028Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2028Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2028Member" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_DebtInstrumentLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentCarryingAmount" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentCarryingAmount"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentCarryingAmount" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DeferredFinanceCostsNet" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DeferredFinanceCostsNet"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DeferredFinanceCostsNet" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentMaturityDate" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentMaturityDate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentMaturityDate" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateEffectivePercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateEffectivePercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateEffectivePercentage" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentConvertibleConversionPrice1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentConvertibleConversionPrice1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentConvertibleConversionPrice1" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="DebtInstrumentConvertibleSharesSubjectToConversion" xlink:href="ions-20260630.xsd#ions_DebtInstrumentConvertibleSharesSubjectToConversion"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="DebtInstrumentConvertibleSharesSubjectToConversion" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage_0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/SegmentInformationTable" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_SegmentReportingAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfSegmentReportingInformationBySegmentTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfSegmentReportingInformationBySegmentTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingAbstract" xlink:to="us-gaap_ScheduleOfSegmentReportingInformationBySegmentTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StatementBusinessSegmentsAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementBusinessSegmentsAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfSegmentReportingInformationBySegmentTable" xlink:to="us-gaap_StatementBusinessSegmentsAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="IonisOperationsMember" xlink:href="ions-20260630.xsd#ions_IonisOperationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementBusinessSegmentsAxis" xlink:to="IonisOperationsMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SegmentReportingInformationLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingInformationLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfSegmentReportingInformationBySegmentTable" xlink:to="us-gaap_SegmentReportingInformationLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CostOfGoodsAndServicesSold" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CostOfGoodsAndServicesSold"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="us-gaap_CostOfGoodsAndServicesSold" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="DrugDiscoveryExpenses" xlink:href="ions-20260630.xsd#ions_DrugDiscoveryExpenses"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="DrugDiscoveryExpenses" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="DrugDevelopmentExpenses" xlink:href="ions-20260630.xsd#ions_DrugDevelopmentExpenses"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="DrugDevelopmentExpenses" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MedicalAffairsExpenses" xlink:href="ions-20260630.xsd#ions_MedicalAffairsExpenses"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="MedicalAffairsExpenses" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ManufacturingAndDevelopmentChemistryExpenses" xlink:href="ions-20260630.xsd#ions_ManufacturingAndDevelopmentChemistryExpenses"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="ManufacturingAndDevelopmentChemistryExpenses" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ResearchAndDevelopmentSupportExpenses" xlink:href="ions-20260630.xsd#ions_ResearchAndDevelopmentSupportExpenses"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="ResearchAndDevelopmentSupportExpenses" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SellingGeneralAndAdministrativeExpense" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SellingGeneralAndAdministrativeExpense"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="us-gaap_SellingGeneralAndAdministrativeExpense" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SegmentReportingOtherItemAmount" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingOtherItemAmount"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="us-gaap_SegmentReportingOtherItemAmount" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingInformationLineItems" xlink:to="us-gaap_NetIncomeLoss" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/OrganizationandBasisofPresentationDetails" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NumberOfOperatingSegments" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NumberOfOperatingSegments"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_NumberOfOperatingSegments" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/RevenuesDetails" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DisaggregationOfRevenueTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:to="us-gaap_DisaggregationOfRevenueTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="OtsukaCollaborationDawnzeraMember" xlink:href="ions-20260630.xsd#ions_OtsukaCollaborationDawnzeraMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="OtsukaCollaborationDawnzeraMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="AstraZenecaCollaborationWainuaMember" xlink:href="ions-20260630.xsd#ions_AstraZenecaCollaborationWainuaMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="AstraZenecaCollaborationWainuaMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DisaggregationOfRevenueLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueTable" xlink:to="us-gaap_DisaggregationOfRevenueLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="AgeOfPediatricPatientsApprovedToUseMedicine" xlink:href="ions-20260630.xsd#ions_AgeOfPediatricPatientsApprovedToUseMedicine"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueLineItems" xlink:to="AgeOfPediatricPatientsApprovedToUseMedicine" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="UpfrontPaymentReceived" xlink:href="ions-20260630.xsd#ions_UpfrontPaymentReceived"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueLineItems" xlink:to="UpfrontPaymentReceived" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NumberOfMaterialComponents" xlink:href="ions-20260630.xsd#ions_NumberOfMaterialComponents"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueLineItems" xlink:to="NumberOfMaterialComponents" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RevenueFromContractWithCustomerNumberOfSeparatePerformanceObligations" xlink:href="ions-20260630.xsd#ions_RevenueFromContractWithCustomerNumberOfSeparatePerformanceObligations"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueLineItems" xlink:to="RevenueFromContractWithCustomerNumberOfSeparatePerformanceObligations" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RevenueFromContractWithCustomerTransactionPrice" xlink:href="ions-20260630.xsd#ions_RevenueFromContractWithCustomerTransactionPrice"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueLineItems" xlink:to="RevenueFromContractWithCustomerTransactionPrice" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="PercentageOfCostsAssociatedWithOngoingGlobalPhase3DevelopmentProgramPaidByCollaborationPartner" xlink:href="ions-20260630.xsd#ions_PercentageOfCostsAssociatedWithOngoingGlobalPhase3DevelopmentProgramPaidByCollaborationPartner"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueLineItems" xlink:to="PercentageOfCostsAssociatedWithOngoingGlobalPhase3DevelopmentProgramPaidByCollaborationPartner" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="PercentageOfCostsForDevelopmentActivitiesToSupportUsRegulatoryApprovalsPaidByCollaborationPartner" xlink:href="ions-20260630.xsd#ions_PercentageOfCostsForDevelopmentActivitiesToSupportUsRegulatoryApprovalsPaidByCollaborationPartner"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueLineItems" xlink:to="PercentageOfCostsForDevelopmentActivitiesToSupportUsRegulatoryApprovalsPaidByCollaborationPartner" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="PercentageOfCostsForDevelopmentActivitiesToSupportGlobalRegulatoryApprovalsPaidByCollaborationPartner" xlink:href="ions-20260630.xsd#ions_PercentageOfCostsForDevelopmentActivitiesToSupportGlobalRegulatoryApprovalsPaidByCollaborationPartner"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisaggregationOfRevenueLineItems" xlink:to="PercentageOfCostsForDevelopmentActivitiesToSupportGlobalRegulatoryApprovalsPaidByCollaborationPartner" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsBiogen" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="BiogenCollaboration2017SpinalMuscularAtrophyMember" xlink:href="ions-20260630.xsd#ions_BiogenCollaboration2017SpinalMuscularAtrophyMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="BiogenCollaboration2017SpinalMuscularAtrophyMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="BiogenCollaboration2018NeurologyMember" xlink:href="ions-20260630.xsd#ions_BiogenCollaboration2018NeurologyMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="BiogenCollaboration2018NeurologyMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="BiogenCollaborationsMember" xlink:href="ions-20260630.xsd#ions_BiogenCollaborationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="BiogenCollaborationsMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_ProductOrServiceAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductOrServiceAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_ProductOrServiceAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_ProductsAndServicesDomain" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductsAndServicesDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="srt_ProductsAndServicesDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="SalanersenMember" xlink:href="ions-20260630.xsd#ions_SalanersenMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="SalanersenMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NextPaymentToBeAchieved" xlink:href="ions-20260630.xsd#ions_NextPaymentToBeAchieved"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="NextPaymentToBeAchieved" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CumulativePaymentsReceived" xlink:href="ions-20260630.xsd#ions_CumulativePaymentsReceived"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="CumulativePaymentsReceived" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiability" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerLiability"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsGSK" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="GlaxoSmithKlineCollaborationMember" xlink:href="ions-20260630.xsd#ions_GlaxoSmithKlineCollaborationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="GlaxoSmithKlineCollaborationMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RegulatoryAgencyAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RegulatoryAgencyAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_RegulatoryAgencyAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RegulatoryAgencyDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RegulatoryAgencyDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RegulatoryAgencyAxis" xlink:to="us-gaap_RegulatoryAgencyDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="JapaneseMinistryOfHealthLaborAndWelfareMember" xlink:href="ions-20260630.xsd#ions_JapaneseMinistryOfHealthLaborAndWelfareMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RegulatoryAgencyAxis" xlink:to="JapaneseMinistryOfHealthLaborAndWelfareMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="EuropeanMedicinesAgencyMember" xlink:href="ions-20260630.xsd#ions_EuropeanMedicinesAgencyMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RegulatoryAgencyAxis" xlink:to="EuropeanMedicinesAgencyMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_RangeAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_RangeAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_RangeMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="0.0"/>
    <loc xlink:type="locator" xlink:label="srt_MinimumMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MinimumMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_MinimumMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_MaximumMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MaximumMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_MaximumMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfPaymentsReceivableOverTermOfCollaboration" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfPaymentsReceivableOverTermOfCollaboration"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfPaymentsReceivableOverTermOfCollaboration" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfLicenseFeesOverTermOfCollaboration" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfLicenseFeesOverTermOfCollaboration"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfLicenseFeesOverTermOfCollaboration" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfDevelopmentMilestonePaymentsOverTermOfCollaboration" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfDevelopmentMilestonePaymentsOverTermOfCollaboration"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfDevelopmentMilestonePaymentsOverTermOfCollaboration" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfRegulatoryMilestonePaymentsOverTermOfCollaboration" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfRegulatoryMilestonePaymentsOverTermOfCollaboration"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfRegulatoryMilestonePaymentsOverTermOfCollaboration" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfSalesMilestonePaymentsOverTermOfCollaboration" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfSalesMilestonePaymentsOverTermOfCollaboration"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfSalesMilestonePaymentsOverTermOfCollaboration" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RoyaltyPercentageReceivedOnNetSalesOfMedicine" xlink:href="ions-20260630.xsd#ions_RoyaltyPercentageReceivedOnNetSalesOfMedicine"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="RoyaltyPercentageReceivedOnNetSalesOfMedicine" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NextPaymentToBeAchieved" xlink:href="ions-20260630.xsd#ions_NextPaymentToBeAchieved"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="NextPaymentToBeAchieved" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CumulativePaymentsReceived" xlink:href="ions-20260630.xsd#ions_CumulativePaymentsReceived"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="CumulativePaymentsReceived" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiability" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerLiability"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsOno" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_ProductOrServiceAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductOrServiceAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_ProductOrServiceAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_ProductsAndServicesDomain" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductsAndServicesDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="srt_ProductsAndServicesDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="SapablursenMember" xlink:href="ions-20260630.xsd#ions_SapablursenMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="SapablursenMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_RangeAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_RangeAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_RangeMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="0.0"/>
    <loc xlink:type="locator" xlink:label="srt_MinimumMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MinimumMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_MinimumMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="OnoCollaborationMember" xlink:href="ions-20260630.xsd#ions_OnoCollaborationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="OnoCollaborationMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NextPaymentToBeAchieved" xlink:href="ions-20260630.xsd#ions_NextPaymentToBeAchieved"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="NextPaymentToBeAchieved" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CumulativePaymentsReceived" xlink:href="ions-20260630.xsd#ions_CumulativePaymentsReceived"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="CumulativePaymentsReceived" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiability" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerLiability"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsOtsuka" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" order="0.0"/>
    <loc xlink:type="locator" xlink:label="OtsukaCollaborationDawnzeraMember" xlink:href="ions-20260630.xsd#ions_OtsukaCollaborationDawnzeraMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="OtsukaCollaborationDawnzeraMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="OtsukaCollaborationsMember" xlink:href="ions-20260630.xsd#ions_OtsukaCollaborationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="OtsukaCollaborationsMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_RangeAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_RangeAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_RangeMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="0.0"/>
    <loc xlink:type="locator" xlink:label="srt_MinimumMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MinimumMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_MinimumMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NextPaymentToBeAchieved" xlink:href="ions-20260630.xsd#ions_NextPaymentToBeAchieved"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="NextPaymentToBeAchieved" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NumberOfMajorEuropeanCountriesRequiredToReceiveReimbursementApproval" xlink:href="ions-20260630.xsd#ions_NumberOfMajorEuropeanCountriesRequiredToReceiveReimbursementApproval"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="NumberOfMajorEuropeanCountriesRequiredToReceiveReimbursementApproval" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NumberOfMajorEuropeanCountries" xlink:href="ions-20260630.xsd#ions_NumberOfMajorEuropeanCountries"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="NumberOfMajorEuropeanCountries" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CumulativePaymentsReceived" xlink:href="ions-20260630.xsd#ions_CumulativePaymentsReceived"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="CumulativePaymentsReceived" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiability" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerLiability"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsRecordati" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="RecordatiAgCollaborationMember" xlink:href="ions-20260630.xsd#ions_RecordatiAgCollaborationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RecordatiAgCollaborationMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_ProductOrServiceAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductOrServiceAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_ProductOrServiceAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_ProductsAndServicesDomain" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductsAndServicesDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="srt_ProductsAndServicesDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="LicenseOfZilganersenMember" xlink:href="ions-20260630.xsd#ions_LicenseOfZilganersenMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="LicenseOfZilganersenMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ResearchAndDevelopmentServicesForZilganersenMember" xlink:href="ions-20260630.xsd#ions_ResearchAndDevelopmentServicesForZilganersenMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="ResearchAndDevelopmentServicesForZilganersenMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ZilganersenMember" xlink:href="ions-20260630.xsd#ions_ZilganersenMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="ZilganersenMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SubsequentEventTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_SubsequentEventTypeAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SubsequentEventTypeDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventTypeDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SubsequentEventTypeAxis" xlink:to="us-gaap_SubsequentEventTypeDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SubsequentEventMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SubsequentEventTypeAxis" xlink:to="us-gaap_SubsequentEventMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfPaymentsReceivableOverTermOfCollaboration" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfPaymentsReceivableOverTermOfCollaboration"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfPaymentsReceivableOverTermOfCollaboration" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfUpfrontPaymentsOverTermOfCollaboration" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfUpfrontPaymentsOverTermOfCollaboration"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfUpfrontPaymentsOverTermOfCollaboration" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfRegulatoryMilestonePaymentsOverTermOfCollaboration" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfRegulatoryMilestonePaymentsOverTermOfCollaboration"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfRegulatoryMilestonePaymentsOverTermOfCollaboration" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfSalesMilestonePaymentsOverTermOfCollaboration" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfSalesMilestonePaymentsOverTermOfCollaboration"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfSalesMilestonePaymentsOverTermOfCollaboration" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RoyaltyPercentageReceivedOnNetSalesOfMedicineDescription" xlink:href="ions-20260630.xsd#ions_RoyaltyPercentageReceivedOnNetSalesOfMedicineDescription"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="RoyaltyPercentageReceivedOnNetSalesOfMedicineDescription" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="UpfrontPaymentReceived" xlink:href="ions-20260630.xsd#ions_UpfrontPaymentReceived"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="UpfrontPaymentReceived" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="NextPaymentToBeAchieved" xlink:href="ions-20260630.xsd#ions_NextPaymentToBeAchieved"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="NextPaymentToBeAchieved" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RevenueFromContractWithCustomerNumberOfSeparatePerformanceObligations" xlink:href="ions-20260630.xsd#ions_RevenueFromContractWithCustomerNumberOfSeparatePerformanceObligations"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="RevenueFromContractWithCustomerNumberOfSeparatePerformanceObligations" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="RevenueFromContractWithCustomerTransactionPrice" xlink:href="ions-20260630.xsd#ions_RevenueFromContractWithCustomerTransactionPrice"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="RevenueFromContractWithCustomerTransactionPrice" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiability" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerLiability"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" order="10.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/CollaborativeArrangementsandLicensingAgreementsDetailsRoche" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:href="ions-20260630.xsd#ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CollaborativeArrangementsAndLicensingAgreementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="RocheCollaborationsMember" xlink:href="ions-20260630.xsd#ions_RocheCollaborationsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RocheCollaborationsMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RocheCollaborationSefaxersenForComplementMediatedDiseasesMember" xlink:href="ions-20260630.xsd#ions_RocheCollaborationSefaxersenForComplementMediatedDiseasesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RocheCollaborationSefaxersenForComplementMediatedDiseasesMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RocheCollaborationRNATargetedProgramsForADAndHDMember" xlink:href="ions-20260630.xsd#ions_RocheCollaborationRNATargetedProgramsForADAndHDMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RocheCollaborationRNATargetedProgramsForADAndHDMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_RangeAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_RangeAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_RangeMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="0.0"/>
    <loc xlink:type="locator" xlink:label="srt_MinimumMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MinimumMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_MinimumMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NumberOfCollaborationAgreements" xlink:href="ions-20260630.xsd#ions_NumberOfCollaborationAgreements"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="NumberOfCollaborationAgreements" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NextPaymentToBeAchieved" xlink:href="ions-20260630.xsd#ions_NextPaymentToBeAchieved"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="NextPaymentToBeAchieved" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="CumulativePaymentsReceived" xlink:href="ions-20260630.xsd#ions_CumulativePaymentsReceived"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="CumulativePaymentsReceived" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiability" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerLiability"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/BasicandDilutedNetIncomeLossPerShareDetails" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="us-gaap_DebtInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2028Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2028Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2028Member" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2026Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2026Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2026Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2030Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2030Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2030Member" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EarningsPerShareBasicLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareBasicLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="us-gaap_EarningsPerShareBasicLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/InvestmentsDetails" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_InvestmentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsAbstract" xlink:to="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FinancialInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinancialInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable" xlink:to="us-gaap_FinancialInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="EquitySecuritiesPrivatelyHeldInvesteeThatBecamePubliclyTradedEntityMember" xlink:href="ions-20260630.xsd#ions_EquitySecuritiesPrivatelyHeldInvesteeThatBecamePubliclyTradedEntityMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="EquitySecuritiesPrivatelyHeldInvesteeThatBecamePubliclyTradedEntityMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsTable" xlink:to="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="AvailableForSaleSecuritiesDebtMaturitiesWithinTwoYearsPercentage" xlink:href="ions-20260630.xsd#ions_AvailableForSaleSecuritiesDebtMaturitiesWithinTwoYearsPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="AvailableForSaleSecuritiesDebtMaturitiesWithinTwoYearsPercentage" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumContractMaturityPeriodRange2" xlink:href="ions-20260630.xsd#ions_MaximumContractMaturityPeriodRange2"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="MaximumContractMaturityPeriodRange2" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NumberOfPrivatelyHeldCompaniesInWhichEntityHasEquityInvestment" xlink:href="ions-20260630.xsd#ions_NumberOfPrivatelyHeldCompaniesInWhichEntityHasEquityInvestment"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="NumberOfPrivatelyHeldCompaniesInWhichEntityHasEquityInvestment" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NumberOfPubliclyHeldCompaniesInWhichEntityHasEquityInvestment" xlink:href="ions-20260630.xsd#ions_NumberOfPubliclyHeldCompaniesInWhichEntityHasEquityInvestment"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="NumberOfPubliclyHeldCompaniesInWhichEntityHasEquityInvestment" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="TermOfContractualSaleRestriction" xlink:href="ions-20260630.xsd#ions_TermOfContractualSaleRestriction"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfTradingSecuritiesAndOtherTradingAssetsLineItems" xlink:to="TermOfContractualSaleRestriction" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/FairValueMeasurementsDetails" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueDisclosuresAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueByMeasurementFrequencyAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByMeasurementFrequencyAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementFrequencyDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueMeasurementFrequencyDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementFrequencyDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsRecurringMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueMeasurementsRecurringMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementsRecurringMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByFairValueHierarchyLevelAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel2Member" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueInputsLevel2Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueInputsLevel2Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_DebtInstrumentAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2030Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2030Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2030Member" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2028Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2028Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2028Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2026Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2026Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2026Member" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NotesPayableFairValueDisclosure" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NotesPayableFairValueDisclosure"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_NotesPayableFairValueDisclosure" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/StockbasedCompensationExpenseDetails" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AwardTypeAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AwardTypeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeStockOptionMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockOptionMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_EmployeeStockOptionMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RestrictedStockUnitsRSUMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RestrictedStockUnitsRSUMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_RestrictedStockUnitsRSUMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_PerformanceSharesMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PerformanceSharesMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_PerformanceSharesMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AwardDateAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AwardDateAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardDateAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_AwardDateDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AwardDateDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardDateAxis" xlink:to="us-gaap_AwardDateDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="GrantedIn2026Member" xlink:href="ions-20260630.xsd#ions_GrantedIn2026Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardDateAxis" xlink:to="GrantedIn2026Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="GrantedIn2025Member" xlink:href="ions-20260630.xsd#ions_GrantedIn2025Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardDateAxis" xlink:to="GrantedIn2025Member" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_GranteeStatusAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GranteeStatusAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_GranteeStatusAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_GranteeStatusDomain" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GranteeStatusDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GranteeStatusAxis" xlink:to="us-gaap_GranteeStatusDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedPaymentArrangementEmployeeMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedPaymentArrangementEmployeeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GranteeStatusAxis" xlink:to="us-gaap_ShareBasedPaymentArrangementEmployeeMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedPaymentArrangementNonemployeeMember" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedPaymentArrangementNonemployeeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GranteeStatusAxis" xlink:to="us-gaap_ShareBasedPaymentArrangementNonemployeeMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_ExecutiveOfficerMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ExecutiveOfficerMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GranteeStatusAxis" xlink:to="srt_ExecutiveOfficerMember" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_RangeAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="srt_RangeAxis" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_RangeMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="0.0"/>
    <loc xlink:type="locator" xlink:label="srt_MinimumMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MinimumMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_MinimumMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_MaximumMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MaximumMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_MaximumMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NumberOfNewMembersAppointedToBoardOfDirectors" xlink:href="ions-20260630.xsd#ions_NumberOfNewMembersAppointedToBoardOfDirectors"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="NumberOfNewMembersAppointedToBoardOfDirectors" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="NumberOfMembersRetiringFromBoardOfDirectors" xlink:href="ions-20260630.xsd#ions_NumberOfMembersRetiringFromBoardOfDirectors"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="NumberOfMembersRetiringFromBoardOfDirectors" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfUnitsGuaranteedToVest" xlink:href="ions-20260630.xsd#ions_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfUnitsGuaranteedToVest"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfUnitsGuaranteedToVest" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfUnitsGuaranteedToVest" xlink:href="ions-20260630.xsd#ions_ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfUnitsGuaranteedToVest"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfUnitsGuaranteedToVest" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/LiabilityRelatedtoSaleofFutureRoyaltiesDetails" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherLiabilitiesDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherLiabilitiesDisclosureAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TypeOfArrangementAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="RoyaltyPurchaseAgreementMember" xlink:href="ions-20260630.xsd#ions_RoyaltyPurchaseAgreementMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="RoyaltyPurchaseAgreementMember" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_ProductOrServiceAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductOrServiceAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_ProductOrServiceAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_ProductsAndServicesDomain" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductsAndServicesDomain"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="srt_ProductsAndServicesDomain" order="0.0"/>
    <loc xlink:type="locator" xlink:label="SpinrazaMember" xlink:href="ions-20260630.xsd#ions_SpinrazaMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="SpinrazaMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="PelacarsenMember" xlink:href="ions-20260630.xsd#ions_PelacarsenMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ProductOrServiceAxis" xlink:to="PelacarsenMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_RangeAxis" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_RangeAxis" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="srt_RangeMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="0.0"/>
    <loc xlink:type="locator" xlink:label="srt_MinimumMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MinimumMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_MinimumMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="srt_MaximumMember" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MaximumMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_MaximumMember" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="UpfrontRoyaltyPaymentReceived" xlink:href="ions-20260630.xsd#ions_UpfrontRoyaltyPaymentReceived"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="UpfrontRoyaltyPaymentReceived" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfPaymentsReceivableForAdditionalMilestones" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfPaymentsReceivableForAdditionalMilestones"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfPaymentsReceivableForAdditionalMilestones" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="PercentageOfRoyaltyPaymentsPaidOnAnnualSalesOfMedicine" xlink:href="ions-20260630.xsd#ions_PercentageOfRoyaltyPaymentsPaidOnAnnualSalesOfMedicine"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="PercentageOfRoyaltyPaymentsPaidOnAnnualSalesOfMedicine" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumAmountOfAnnualSalesOnWhichRoyaltyPaymentsArePaid" xlink:href="ions-20260630.xsd#ions_MaximumAmountOfAnnualSalesOnWhichRoyaltyPaymentsArePaid"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumAmountOfAnnualSalesOnWhichRoyaltyPaymentsArePaid" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="MaximumRoyaltyPaymentsMadeBeforeRoyaltyInterestRevertsBack" xlink:href="ions-20260630.xsd#ions_MaximumRoyaltyPaymentsMadeBeforeRoyaltyInterestRevertsBack"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="MaximumRoyaltyPaymentsMadeBeforeRoyaltyInterestRevertsBack" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="PaymentsForTransactionCostsRelatedToSaleOfFutureRoyalties" xlink:href="ions-20260630.xsd#ions_PaymentsForTransactionCostsRelatedToSaleOfFutureRoyalties"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="PaymentsForTransactionCostsRelatedToSaleOfFutureRoyalties" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateEffectivePercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateEffectivePercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateEffectivePercentage" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/ConvertibleDebtDetails" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_DebtDisclosureAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtDisclosureAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentTable" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_DebtInstrumentTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_DebtInstrumentAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2030Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2030Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2030Member" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2028Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2028Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2028Member" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ConvertibleSeniorNotesDue2026Member" xlink:href="ions-20260630.xsd#ions_ConvertibleSeniorNotesDue2026Member"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="ConvertibleSeniorNotesDue2026Member" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentLineItems" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_DebtInstrumentLineItems" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_DebtInstrumentFaceAmount" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentFaceAmount"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentFaceAmount" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_RepaymentsOfConvertibleDebt" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RepaymentsOfConvertibleDebt"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_RepaymentsOfConvertibleDebt" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesConversionOfConvertibleSecurities" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodSharesConversionOfConvertibleSecurities"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesConversionOfConvertibleSecurities" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="DebtInstrumentConvertibleConversionPriceIncludingCallSpread" xlink:href="ions-20260630.xsd#ions_DebtInstrumentConvertibleConversionPriceIncludingCallSpread"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="DebtInstrumentConvertibleConversionPriceIncludingCallSpread" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="SharesReceivedFromExerciseOfNoteHedges" xlink:href="ions-20260630.xsd#ions_SharesReceivedFromExerciseOfNoteHedges"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="SharesReceivedFromExerciseOfNoteHedges" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="RetirementOfSharesReceivedFromExerciseOfBondHedgesShares" xlink:href="ions-20260630.xsd#ions_RetirementOfSharesReceivedFromExerciseOfBondHedgesShares"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="RetirementOfSharesReceivedFromExerciseOfBondHedgesShares" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <loc xlink:type="locator" xlink:label="DebtInstrumentConvertiblePercentageOfPrincipalAmountUsedAsPurchasePriceUponOccurrenceOfFundamentalChange" xlink:href="ions-20260630.xsd#ions_DebtInstrumentConvertiblePercentageOfPrincipalAmountUsedAsPurchasePriceUponOccurrenceOfFundamentalChange"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="DebtInstrumentConvertiblePercentageOfPrincipalAmountUsedAsPurchasePriceUponOccurrenceOfFundamentalChange" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/SegmentInformationDetails" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="us-gaap_SegmentReportingAbstract" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingAbstract"/>
    <loc xlink:type="locator" xlink:label="us-gaap_NumberOfReportableSegments" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NumberOfReportableSegments"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingAbstract" xlink:to="us-gaap_NumberOfReportableSegments" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="us-gaap_SegmentReportingOtherItemCompositionDescription" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingOtherItemCompositionDescription"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SegmentReportingAbstract" xlink:to="us-gaap_SegmentReportingOtherItemCompositionDescription" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://xbrl.sec.gov/ecd/role/InsiderTradingArrangements" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="ecd_InsiderTradingArrLineItems" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_InsiderTradingArrLineItems"/>
    <loc xlink:type="locator" xlink:label="ecd_TradingArrByIndTable" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_TradingArrByIndTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_InsiderTradingArrLineItems" xlink:to="ecd_TradingArrByIndTable" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ecd_IndividualAxis" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_IndividualAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_TradingArrByIndTable" xlink:to="ecd_IndividualAxis" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ecd_AllIndividualsMember" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_AllIndividualsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_IndividualAxis" xlink:to="ecd_AllIndividualsMember" order="0.0"/>
    <loc xlink:type="locator" xlink:label="ShannonDeversMember" xlink:href="ions-20260630.xsd#ions_ShannonDeversMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_IndividualAxis" xlink:to="ShannonDeversMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ecd_TradingArrAxis" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_TradingArrAxis"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_TradingArrByIndTable" xlink:to="ecd_TradingArrAxis" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <loc xlink:type="locator" xlink:label="ecd_AllTradingArrangementsMember" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_AllTradingArrangementsMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_TradingArrAxis" xlink:to="ecd_AllTradingArrangementsMember" order="0.0"/>
    <loc xlink:type="locator" xlink:label="TerminationMember" xlink:href="ions-20260630.xsd#ions_TerminationMember"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_TradingArrAxis" xlink:to="TerminationMember" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ecd_MtrlTermsOfTrdArrTextBlock" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_MtrlTermsOfTrdArrTextBlock"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_InsiderTradingArrLineItems" xlink:to="ecd_MtrlTermsOfTrdArrTextBlock" order="1.01" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ecd_NonRule10b51ArrTrmntdFlag" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_NonRule10b51ArrTrmntdFlag"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_InsiderTradingArrLineItems" xlink:to="ecd_NonRule10b51ArrTrmntdFlag" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ecd_TrdArrIndName" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_TrdArrIndName"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_InsiderTradingArrLineItems" xlink:to="ecd_TrdArrIndName" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ecd_TrdArrIndTitle" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_TrdArrIndTitle"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_InsiderTradingArrLineItems" xlink:to="ecd_TrdArrIndTitle" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ecd_TrdArrTerminationDate" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_TrdArrTerminationDate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_InsiderTradingArrLineItems" xlink:to="ecd_TrdArrTerminationDate" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ecd_Rule10b51ArrTrmntdFlag" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_Rule10b51ArrTrmntdFlag"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_InsiderTradingArrLineItems" xlink:to="ecd_Rule10b51ArrTrmntdFlag" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="ecd_TrdArrExpirationDate" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_TrdArrExpirationDate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ecd_InsiderTradingArrLineItems" xlink:to="ecd_TrdArrExpirationDate" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
  <presentationLink xlink:role="http://ionis.com/role/DocumentAndEntityInformation" xlink:type="extended">
    <loc xlink:type="locator" xlink:label="DocumentAndEntityInformationAbstract" xlink:href="ions-20260630.xsd#ions_DocumentAndEntityInformationAbstract"/>
    <loc xlink:type="locator" xlink:label="dei_DocumentInformationTable" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_DocumentInformationTable"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="dei_DocumentInformationTable" order="1.0"/>
    <loc xlink:type="locator" xlink:label="dei_DocumentInformationLineItems" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_DocumentInformationLineItems"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationTable" xlink:to="dei_DocumentInformationLineItems" order="1.0"/>
    <loc xlink:type="locator" xlink:label="dei_EntityCentralIndexKey" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityCentralIndexKey"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityCentralIndexKey" order="0.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_DocumentType" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_DocumentType"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_DocumentType" order="1.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_DocumentQuarterlyReport" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_DocumentQuarterlyReport"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_DocumentQuarterlyReport" order="2.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_DocumentPeriodEndDate" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_DocumentPeriodEndDate"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_DocumentPeriodEndDate" order="3.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_DocumentFiscalYearFocus" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_DocumentFiscalYearFocus"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_DocumentFiscalYearFocus" order="4.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_DocumentTransitionReport" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_DocumentTransitionReport"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_DocumentTransitionReport" order="5.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityFileNumber" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityFileNumber"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityFileNumber" order="6.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityRegistrantName" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityRegistrantName"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityRegistrantName" order="7.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityIncorporationStateCountryCode" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityIncorporationStateCountryCode"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityIncorporationStateCountryCode" order="8.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityTaxIdentificationNumber" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityTaxIdentificationNumber"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityTaxIdentificationNumber" order="9.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityAddressAddressLine1" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityAddressAddressLine1"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityAddressAddressLine1" order="10.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityAddressCityOrTown" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityAddressCityOrTown"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityAddressCityOrTown" order="11.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityAddressStateOrProvince" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityAddressStateOrProvince"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityAddressStateOrProvince" order="12.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityAddressPostalZipCode" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityAddressPostalZipCode"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityAddressPostalZipCode" order="13.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_CityAreaCode" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_CityAreaCode"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_CityAreaCode" order="14.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_LocalPhoneNumber" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_LocalPhoneNumber"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_LocalPhoneNumber" order="15.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_Security12bTitle" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_Security12bTitle"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_Security12bTitle" order="16.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_TradingSymbol" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_TradingSymbol"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_TradingSymbol" order="17.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_SecurityExchangeName" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_SecurityExchangeName"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_SecurityExchangeName" order="18.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityCurrentReportingStatus" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityCurrentReportingStatus"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityCurrentReportingStatus" order="19.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityInteractiveDataCurrent" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityInteractiveDataCurrent"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityInteractiveDataCurrent" order="20.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityFilerCategory" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityFilerCategory"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityFilerCategory" order="21.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntitySmallBusiness" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntitySmallBusiness"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntitySmallBusiness" order="22.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityEmergingGrowthCompany" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityEmergingGrowthCompany"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityEmergingGrowthCompany" order="23.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityShellCompany" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityShellCompany"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityShellCompany" order="24.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_EntityCommonStockSharesOutstanding" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityCommonStockSharesOutstanding"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_EntityCommonStockSharesOutstanding" order="25.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_AmendmentFlag" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_AmendmentFlag"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_AmendmentFlag" order="26.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_DocumentFiscalPeriodFocus" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_DocumentFiscalPeriodFocus"/>
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_DocumentFiscalPeriodFocus" order="27.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <loc xlink:type="locator" xlink:label="dei_CurrentFiscalYearEndDate" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_CurrentFiscalYearEndDate"/>
<!-- [WMV7][J/NJffTQVRI9FpE9QfYvTvI5B4RWmy+DoDBmFnnLBGzq3J6ROubYEvn/27P0CucjsBwuF6oQ62qjvQlEjQQ8ZLY94FOWwe4FVkjED/w4Y+VDYJ/kQEJtUP0Ooq11pZclwfECJ4Ip8e+d/gLlaHLSPs4KHnPSpJs9pVqD1w3GOHwcXkaj3yLrnuBQOHaHcwlC82Ob/c8FRNoarskCzEhm38WmuU3BuOVjum4BLE/rLhov6xqpuaKucE12nFAr9o1oB11AnHeWG1XjGtAj3SiV3LIcG/TkQhFCf44/gwfrqLrWic3ykdpvsflj+L6PA03BR9gkvPVl] CSR-->
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_DocumentInformationLineItems" xlink:to="dei_CurrentFiscalYearEndDate" order="28.0" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </presentationLink>
</linkbase>
