Exhibit 5.1

Seaport West 155 Seaport Boulevard Boston, MA 02210-2600   617 832 1000 main 617 832 7000 fax

March 23, 2022

Applied Genetic Technologies Corporation

14193 NW 119th Terrace, Suite 10

Alachua, FL 32615

Re: Registration Statement on Form S-3

Ladies and Gentlemen:

We have acted as counsel to Applied Genetic Technologies Corporation, a Delaware corporation (the “Company”), in connection with the offer and sale of up to 8,625,000 shares (the “Shares”) of the Company’s common stock, par value $0.001 per share (the “Common Stock”), pursuant to the Company’s prospectus supplement dated March 22, 2022 filed with the Commission pursuant to Rule 424(b) under the Securities Act of 1933, as amended (the “Securities Act”), with the accompanying base prospectus dated April 12, 2021 (together, the “Prospectus”), both of which form part of the Company’s Registration Statement on Form S-3 (Registration No. 333-255008) initially filed with the Commission on April 2, 2021 (as amended, the “Registration Statement”).

We are familiar with the proceedings of the Board of Directors of the Company on March 3, 2022 and its Pricing Committee on March 22, 2022 in connection with the authorization, issuance and sale of the Shares. We have examined such matters of fact and questions of law as we have considered appropriate for the purposes of this letter. We have relied upon certificates and other assurances of officers of the Company and others as to factual matters without having independently verified such factual matters. In our examination, we have assumed the genuineness of all signatures, the authenticity of all documents submitted to us as originals, the conformity to authentic original documents of all documents submitted to us as copies and the due authorization, execution and delivery of all documents by all persons other than the Company where authorization, execution and delivery are prerequisites to the effectiveness of such documents.

The opinion expressed below is limited to the General Corporation Law of the State of Delaware.

On the basis of the foregoing, it is our opinion that, as of the date hereof, the Shares have been duly authorized and, when issued and delivered by the Company against payment therefor as set forth in the Prospectus, will be validly issued, fully paid and non-assessable.

Applied Genetic Technologies Corporation

March 23, 2022

Page 2

This opinion is being delivered solely for the benefit of the Company and such other persons as are entitled to rely upon it pursuant to the applicable provisions of the Securities Act. This opinion may not be used, quoted, relied upon or referred to for any other purpose, nor may this opinion be used, quoted, relied upon or referred to by any other person, for any purpose, without our prior written consent.

We consent to your filing this opinion as an exhibit to a Current Report on Form 8-K to be filed with the Commission for incorporation by reference into the Registration Statement and to the reference to our firm in the Prospectus under the heading “Legal Matters.” In giving such consent, we do not thereby admit that we are in the category of persons whose consent is required under Section 7 of the Securities Act or the rules and regulations of the Commission thereunder.

Very truly yours,
FOLEY HOAG LLP
By:	/s/ Stacie S. Aarestad
	a Partner