Applied DNA Sciences, Inc. (the “Company”) is filing this Amendment No. 1 (the “Amendment”) to its Annual Report on Form 10-K for the fiscal year ended September 30, 2013, previously filed with the Securities and Exchange Commission (the “SEC”) on December 20, 2013 (the “Original 10-K”). The Company has determined that as a result of the Company’s transition from a “smaller reporting company” to an “accelerated filer” at the end of fiscal 2013, the Company was required to include in the Original 10-K the auditor attestation report on internal control over financial reporting required by Section 404(b) of the Sarbanes-Oxley Act of 2002 (the “Auditor Attestation Report”). This Amendment includes, among other changes and additions to the Original 10-K described below, the Auditor Attestation Report and revisions to Management’s Report on Internal Control over Financial Reporting.

The Company was a smaller reporting company for fiscal year 2013 subject to scaled disclosure requirements afforded to smaller reporting companies. When a company is required to exit smaller reporting company status, as the Company did at the end of fiscal 2013, it may continue to provide scaled disclosure as a smaller reporting company through the filing of the annual report on Form 10-K for that year, but, as an accelerated filer, it is required to include an Auditor Attestation Report. At the time the Company filed the Original 10-K in December 2013, it believed that the contents of the Original 10-K were governed by the disclosure requirements applicable to a smaller reporting company and omitted the Auditor Attestation Report required for an accelerated filer.

In addition to the above, this Amendment includes the following changes and additions to the Original 10-K:

Item 1 “Business- Target Markets” has been updated to clarify and enhance the narrative section based on SEC comments the Company received on February 20, 2014 and March 12, 2014. Certain other conforming changes have been made.

We have included new risk factors relating to possible claims for damages in connection with certain sales of shares of our stock in the open market and the material weakness in internal control over financial reporting identified in Management's Report on Internal Control over Financial Reporting.

Our independent registered public accounting firm has revised their audit report on our consolidated financial statements and added a paragraph regarding their separate audit report on internal control over financial reporting.

We have updated our Notes to our consolidated financial statement on Note M – Subsequent Events.

New certifications by our principal executive officer and principal financial officer under Sections 302 and 906 of Sarbanes-Oxley Act of 2002 are filed as exhibits to this Amendment.

Except as described above, no other amendments have been made to the Original Filing. This Amendment does not modify or update the disclosures or financial information contained in the Original Filing in any way other than as required to reflect the revisions discussed above.

Document Fiscal Year Focus

2013

Document Fiscal Period Focus