Exhibit 5.1

Natera, Inc.

13011 McCallen Pass

Building A, Suite 100

Austin, TX 78753

Ladies and Gentlemen:

We have acted as special counsel to Natera, Inc., a Delaware corporation (the “Company”), in connection with the preparation and filing with the Securities and Exchange Commission (the “Commission”) of a Registration Statement on Form S-3 (the “Registration Statement”) pursuant to the Securities Act of 1933, as amended (the “Securities Act”), relating to the resale from time to time by the selling stockholders described therein (the “Selling Stockholders”) of up to an aggregate of 68,023 shares of the Company’s common stock, par value $0.0001 per share (the “Common Stock”), which consist of (i) 45,533 shares (the “Closing Shares”) of the Common Stock issued to the Selling Stockholders on or about November 10, 2026, in connection with the closing of the transactions contemplated by the Agreement and Plan of Merger, dated as of November 2, 2026, by and among the Company, two wholly owned merger subsidiaries of the Company, a privately held company and a stockholder representative (the “Merger Agreement”), and (ii) an estimated 22,490 additional shares of the Common Stock that may become issuable to the Selling Stockholders after the closing of the transactions pursuant to the Merger Agreement (the “Potentially Issuable Shares”).

In arriving at the opinion expressed below, we have examined originals, or copies certified or otherwise identified to our satisfaction as being true and complete copies of the originals, of such documents, corporate records, certificates of officers of the Company and of public officials and other instruments as we have deemed necessary or advisable to enable us to render this opinion. In our examination, we have assumed the genuineness of all signatures, the legal capacity and competency of all natural persons, the authenticity of all documents submitted to us as originals and the conformity to original documents of all documents submitted to us as copies. As to any facts material to this opinion, we have relied, to the extent we deemed appropriate and without independent investigation, upon certificates and statements of officers and other representatives of the Company.

Based upon the foregoing, and subject to the assumptions, exceptions, qualifications and limitations set forth herein, we are of the opinion that (i) the Closing Shares have been duly authorized and are validly issued, fully paid and non-assessable, and (ii) the Potentially Issuable Shares, when issued pursuant to the terms of the Merger Agreement, will have been duly authorized and validly issued and will be fully paid and non-assessable.

We consent to the filing of this opinion as an exhibit to the Registration Statement, and we further consent to the use of our name under the caption “Legal Matters” in the Registration Statement and the prospectus that forms a part thereof. In giving these consents, we do not thereby admit that we are within the category of persons whose consent is required under Section 7 of the Securities Act or the rules and regulations of the Commission promulgated thereunder.

Very truly yours,

/s/ Gibson, Dunn & Crutcher LLP