Exhibit 5.1

LAW OFFICES   One Arizona Center 400 East Van Buren Street Suite 1900 Phoenix, AZ 85004-2202 602.382.6000 602.382.6070 (Fax) www.swlaw.com DENVER   LAS VEGAS   LOS ANGELES   LOS CABOS   ORANGE COUNTY   PHOENIX   SALT LAKE CITY   TUCSON

July 29, 2014

Quidel Corporation

12544 High Bluff Drive, Suite 200

San Diego, California 92130

Re: Registration Statement on Form S-8

Ladies and Gentlemen:

We have examined the Registration Statement on Form S-8 (the “Registration Statement”) of Quidel Corporation, a Delaware corporation (the “Company”), filed with the Securities and Exchange Commission (the “Commission”) pursuant to the Securities Act of 1933, as amended (the “Securities Act”), in connection with the offering by the Company of up to an additional 950,000 shares (the “Shares”) of the Company’s common stock, par value $0.001 per share (“Common Stock”), pursuant to the terms of the Company’s Amended and Restated 2010 Equity Incentive Plan (the “2010 Plan”).

We have examined the originals, or photostatic or certified copies, of such records of the Company and certificates of officers of the Company and of public officials and such other documents as we have deemed relevant and necessary as the basis for the opinions set forth below. 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.

Based upon the foregoing examination and in reliance thereon, and subject to the assumptions stated and in reliance on statements of fact contained in the documents that we have examined, we are of the opinion that the Shares, when issued in accordance with the terms of the 2010 Plan against payment therefor, will be validly issued, 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 in appropriate sections of 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.

Very truly yours,

/s/ Snell & Wilmer L.L.P.

Snell & Wilmer is a member of LEX MUNDI, The Leading Association of Independent Law Firms.