SecProbe.io

Mail Stop 6010 Via Facsimile and U.S. Mail

May 1, 2006
  Mr. James Hayward Chief Executive Officer Applied DNA Sciences, Inc.  25 Health Sciences Drive, Suite 113 Stony Brook, NY 10532
Re: Applied DNA Sciences, Inc.
  Amendment No. 7 to Registra tion Statement on Form SB-2
  Filed April 17, 2006   File No. 333-122848

Dear Mr. Hayward:
We have reviewed your filings and have th e following comments.  Where indicated, we
think you should revise your documents in response  to these comments.  If you disagree, we will
consider your explanation as to why our commen t is inapplicable or a revision is unnecessary.
Please be as detailed as necessa ry in your explanation.  In some  of our comments, we may ask
you to provide us with supplemental informati on so we may better understand your disclosure.
After reviewing this information, we ma y or may not raise additional comments.

Please understand that the purpose of our re view process is to assist you in your
compliance with the applicable disclosure requir ements and to enhance the overall disclosure in
your filing.  We look forward to working with you in these respects.  We welcome any questions
you may have about our comments or on any other aspe ct of our review.  Feel free to call us at
the telephone numbers listed at  the end of this letter.

Amendment No. 7 to Registration Statement on Form SB-2

General
 1. Prior to requesting acceleration for effectiv eness, please amend your Form 10-KSB for
the year ended September 30, 2005, as applicab le, to comply with our comments on your
Form SB-2.
 2. Prior to requesting acceleration for effectiv eness, please refer to Item 310(g) of
Regulation S-B and consider whether you need  to include, in an amended registration

Mr. James Hayward
Applied DNA Sciences, Inc. May 1, 2006 Page 2
statement on Form SB-2, unaud ited financial statements for the three and six months
ended March 31, 2006.
 Consolidated Financial Statements

 Index to Financial Statements, page F-1

 3. The index to your financial statements indi cates that the report of your independent
registered public accounting firm is f ound on page F-43; however, the independent
accountant’s report does not appe ar anywhere in the document. Please revise your Form
SB-2 accordingly.
 Consolidated Statements of Cash Flows, page F-56

 4. We acknowledge the information provided in “Exhibit B” in response to comment 14 of
our letter dated January 26, 2006; however, we re iterate our request th at provide to us a
reconciliation between your statement of cash flows and your statement of shareholders’
deficit for the year ended September 30, 2005. In particular, please tell us how the
following line items on your September 30, 2005 statement of cash flows correlate to the
aggregate of the individual transactions on the statement of sh areholders’ deficit:
“common stock issued in exchange for consultant services  rendered”- $14,805,128;
“ESOP shares”- $3,960,000; and “amortizati on of beneficial c onversion feature”-
$8,836,000.
  Notes to (Audited) Consolidated Financial Statements

 Note B- Acquisition of Intangible Assets, page F-64

 5. We acknowledge your response to comment 3 of our letter dated January 26, 2006. You
disclose that you acquired “proprietary DNA anti-counterfeit trade secrets developed by
Biowell,” but then state that there were no projects in place at acquisition or future
research and development activities planned with  respect to the intellectual property that
you acquired from Biowell, which is the ba sis for your assertion that the $14.7 million
did not represent IPRD at acquisition. This  assertion appears c ontradictory to your
“Intellectual Property” discussi on on page 29 and your disclosu re on page 36; that is, it
appears that research and development activi ties are the core of your company’s business
and that there are projects under developm ent that utilize the Biowell intellectual
property. Please revise your statement of operations for the year ended September 30,
2005 to reflect the $14.7 million charge as IPRD or  provide us with further information to
clarify why it is not an IPRD charge pursuant to paragraph 42 of SFAS No. 141.
 6. Additionally, please clarify whether the “dev eloped core technologies” and “developed
product technologies” that you acqui red from Biowell meet the criteria of paragraph 11 c.
of SFAS No. 2.  It appears that you are usi ng these technologies in conjunction with
research and development projects.

Mr. James Hayward
Applied DNA Sciences, Inc. May 1, 2006 Page 3   Note E- Capital Stock, pages F-73 and F-74

 7. Please provide us with a r econciliation of the note conve rsion transactions that you
outlined for the three months ended March 31, 2 005 to those disclosed in Note B of your
Form 10-QSB/A for the period ended March 31, 2005. Based on the information
provided, it appears that you converted $2,246,056 of  your notes payable in exchange for
6,488,051 shares during the three months ended March 31, 2005; however, the disclosure
in Note B of your March 31, 2005 Form 10- QSB/A indicates t hose figures as $4,221,320
and 7,998,551, respectively.
  Note F- Stock Options and Warrants, pages F-77 - F-80

 8. We acknowledge your response to comments 4 and 5 of our letter dated January 26,
2006. Your registration rights ag reement appears to require you to file a registration
statement that is declared effective by the SEC and to keep the registration statement continuously effective for a preset time pe riod, or you are required to pay a liquidated
damages payment equal to 3.5% per month on the face value of the related convertible
notes, with no cap on the maximum penalty that  could be incurred.  The EITF recently
deliberated the impact of these liquidate d damages clauses and the effect on the
accounting and classification of instruments s ubject to the scope of EITF 00-19 in EITF
05-4 The Effect of a Liquidated Damages Cl ause on a Freestanding Financial Instrument
Subject to Issue No. 00-19.   The EITF has not reached a consensus on this issue and has
deferred deliberation until the FASB addresse s certain questions which could impact a
conclusion on this issue; however, different  views on this issue are outlined in Issue
Summary No. 1 to EITF 05-4.  Tell us how you viewed and accounted for the registration
rights agreement and the related warrants.  Please also refer to the Division of
Corporation Finance "Current Accounting and Disclosure Issues" Section II(B) -
Classification and Measurement of Warrants and Embedded Conversion Features (New).
You can find this at the following website: http://www.sec.gov/divisions/corpfin/acctdis120105.pdf.

 9. Additionally, you disclose that your liquidating damages are a “penalty.” This appears to
render your ability to settle in unregistered sh ares an uneconomic alte rnative that you are
precluded from considering in lieu of cash settlement. Considering this, please tell us
how you determined that you could classify the warrants within equity based on the
provisions of EITF No. 00-19.
 10. We acknowledge your response to comments 6 and 7 of our letter dated January 26,
2006. Please provide us with your explicit anal ysis of whether the warrants meet the
definition of a derivative instrument unde r SFAS No. 133, paragraph 6, and provide us
with your corresponding point-by- point analysis of whether th e warrants meet all of the
criteria outlined in paragraphs 12-32 of EITF No. 00-19 in order to qualify for the
paragraph 11a.) scope exception under SFAS No. 133 and ultimately reside in equity.

Mr. James Hayward
Applied DNA Sciences, Inc. May 1, 2006 Page 4  11. We acknowledge your response to comment 9 of our letter da ted January 26, 2006.
Please revise your disclosure to clarify and quantify your accounting for the 3 million
warrants issued to directors and advisors during the three months ended September 30,
2005. That is, tell us whether you initially reco rded the fair value of  the shares within
equity and subsequently valu ed them as a derivative liability under SFAS No. 133 due to
the “cashless exercise” provisions available to the warrant holders, as this is unclear based on your current disclosure. Additionally, please provide us with your explicit analysis of whether the warrants meet the definition of a derivative instrument under
SFAS No. 133, paragraph 6, and provide us  with your corres ponding point-by-point
analysis of whether the warrant s meet all of the criteria out lined in paragraphs 12-32 of
EITF No. 00-19 in order to qualify for the paragraph 11a.) scope exception under SFAS
No. 133 and ultimately reside in equity.

12. In your response to comments 4-7, you repeat edly state that the penalties for the
January/February 2005 warrants an d the July 2005 Trilogy warrant s can be settled in cash
or unregistered shares.  Please tell us w hy you do not believe the shares need to be
registered.  For example, the definition of “r egistrable securities” in paragraph 1.1(i) of
Exhibit 4.4 to your 8-K filed January 28, 2005 for the January/February 2005 convertible
notes offering appears to indi cate that shares issued in  conjunction with the warrant
shares would be “registrable.”   In addition, on page 79, you st ate that you also agreed to
file a registration statement underlying the Tr ilogy warrants and that , in the event Trilogy
successfully brings a claim against you rela ting to this matter, it could result in a
significant decrease in your liquidity or assets, which also alludes to a penalty.

Form 10-QSB for the Fiscal Quarter Ended June 30, 2005

 Condensed Consolidated Statement of Cash Flows, page 17

 13. We acknowledge your response to comment  14 of our letter dated January 26, 2006.
Please provide us with additional information to clarify the errors that you have identified in Exhibit B, as follows:

• Notation A in Exhibit B indicates that  you have “missed” reflecting expense
related to common shares issued in ex change for services rendered by non-
employee consultants of $831,000. Please te ll us whether your statement of
operations for the three months ended June 30, 2005, as presented in your Form
10-QSB, correctly reflected the $831,000 in that period.

• Notation B in Exhibit B indicates that you di d not record the shares issued in your
note conversion transactions at their fair value, whic h would have resulted in
incremental conversion expense. Pl ease reconcile the $4,474,533 in “debt
exchanged for stock” to the statement of  shareholders’ deficit at June 30, 2005
and tell us whether that amount reflec ts non-cash expense, as your response
indicates that you simply offset the net book value of the debt converted to equity

Mr. James Hayward
Applied DNA Sciences, Inc. May 1, 2006 Page 5
and did not record any expense. Please also  tell us the net boo k value of the debt
converted to shares from 1/1/05 thro ugh 6/30/05 and correlate that to the
$4,474,533 and the $(2,313,500).
 Form 10-QSB/A#2 for the Fiscal  Quarter Ended March 31, 2005

 General

 14. As acknowledged in your response to comment  11 of our letter dated January 26, 2006,
prior to requesting acceleration of effectiv eness for your Form SB-2, please amend your
March 31, 2005 Form 10-QSB to appropriately  present the financial statements as
“restated.”
Notes to (Unaudited) Condensed Consolidated Financial Statements

Note B- Capital Stock, page 25
 15. We acknowledge your response to comments 12 and 13 of our letter dated January 26,
2006, inclusive the information provided in “Exh ibit A.” You disclose in Note B that you
retired an aggregate of $4,221,032 in conve rtible notes payable by issuing 7,998,551
shares of your common stock; however, th e information provided in Exhibit A with
respect to the “Lee” transaction, coupled with  your assertion that you did not charge
anything to the statement of operations, indi cates that you did not account for the fair
value of any incremental consideration paid to  retire the convertible notes. Please provide
us with a reconciliation that details each of the note payable convers ion transactions that
you effected during the three months ended March 31, 2005, including: the net book
value of the convertible debt retired; the value of  the shares issued through stockholders’
equity; and any amounts charged to your statement of operations  for the fair value of any
incremental consideration paid.
 16. Additionally, giving considera tion to our comment above, pl ease provide us with the
related restatement disclosures required by paragraph 26 of SFAS No. 154, inclusive of
any revisions to your original restatement of $2.9 million.

* * * * *
As appropriate, please amend your filings in response to these comments.  You may wish
to provide us with marked copies of the amendm ents to expedite our review.  Please furnish a
cover letter with your amendments that keys your responses to our comments and provides any
requested supplemental information.  Detailed cover letters greatly facilitate  our review.  Please
understand that we may have additional comm ents after reviewing your amendments and
responses to our comments.

Mr. James Hayward
Applied DNA Sciences, Inc. May 1, 2006 Page 6
  You may contact Amy Bruckne r, Staff Accountant, at (202) 551-3657 or Mary Mast,
Senior Accountant, at (202) 551- 3613 if you have questions rega rding comments on the financial
statements and related matters.  Please contac t John Krug, Senior Staff Attorney, at (202) 551-
3609 with any other questions.

Sincerely,

Jeffrey P. Riedler
        A s s i s t a n t  D i r e c t o r    cc: Joe Daniels, Esq.
Fulbright & Jaworski LLP  666 Fifth Avenue, 31
st Floor
New York, NY 10103-3198