FIRST AMENDMENT TO WARRANT AGREEMENT

Exhibit 4.1

FIRST AMENDMENT TO WARRANT AGREEMENT

THIS FIRST AMENDMENT TO WARRANT AGREEMENT (this “Amendment”), dated as of April 1, 2015, is by and between Applied DNA Sciences, Inc., a Delaware corporation (the “Company”), and American Stock Transfer & Trust Company, LLC, a New York limited liability trust company, as Warrant Agent (the “Warrant Agent”).

WHEREAS, the Company and the Warrant Agent have previously entered into that certain Warrant Agreement, dated as of November 20, 2014 (the “Warrant Agreement”), and the Company and the Warrant Agent now desire to amend the Warrant Agreement on the terms and subject to the conditions set forth herein (with capitalized terms used and not defined in this Amendment having the respective meanings given them in the Warrant Agreement);

WHEREAS, the Company has filed with the Commission a registration statement on Form S-3 (File No. 333-202432) (the “Shelf Registration Statement”; and together with the Registration Statement, the “Registration Statements”) for the registration under the Securities Act of Common Stock, Warrants and other securities of the Company in an aggregate amount not to exceed $25,000,000; and

WHEREAS, pursuant to an underwriting agreement, dated March 27, 2015, by and between the Company and Maxim Group, LLC, as representatives of the several underwriters named in Schedule I thereto, and a final prospectus supplement, dated March 27, 2015, filed by the Company with the Commission pursuant to Rule 424(b) under the Securities Act (the “Prospectus Supplement”; and together with the Prospectus, the “Prospectuses”), the Company is engaged in a public offering (the “Follow-on Offering”) of shares of Common Stock and Warrants and, in connection therewith, has determined to issue and deliver up to 1,757,200 Warrants (including up to 229,200 Warrants subject to an over-allotment option granted to the underwriters by the Company) to public investors in the Follow-on Offering, each such Warrant evidencing the right of the holder thereof to purchase one share of Common Stock at an exercise price of $3.50 per share, subject to adjustment as described in the Warrant Agreement; and

WHEREAS, the Company desires the Warrant Agent to act on behalf of the Company, and the Warrant Agent is willing to so act, in connection with the issuance, registration, transfer, exchange and exercise of the Warrants to be issued to public investors in the Follow-on Offering; and

WHEREAS, the Company desires to provide for the form and provisions of the Warrants to be issued to public investors in the Follow-on Offering, the terms upon which they shall be issued and exercised, and the respective rights, limitation of rights, and immunities of the Company, the Warrant Agent, and the Holders; and

WHEREAS, all acts and things have been done and performed which are necessary to make the Warrants to be issued to public investors in the Follow-on Offering, when executed on behalf of the Company and countersigned by or on behalf of the Warrant Agent, as provided herein, the valid, binding and legal obligations of the Company, and to authorize the execution and delivery of this Agreement.

 NOW, THEREFORE, in consideration of the mutual agreements herein contained, the parties hereto agree as follows:

[Signature Page Follows]

IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be duly executed as of the date first above written.

Signature Page to Amendment to Warrant Agreement by and between Applied DNA Sciences, Inc.

and American Stock Transfer & Trust Company, LLC, as Warrant Agent