
Delaware		98-0379351

(State or other jurisdiction of incorporation or organization)		(I.R.S. Employer Identification No.)

9 Commercial Blvd., Suite 200, Novato, CA		94949

(Address of principal executive offices)		(Zip Code)

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes o No X

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes o No X

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes X No o

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting company. See definition of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act). Yes o No X

The aggregate market value of the voting stock held by non-affiliates of the registrant as of April 9, 2009 was approximately $10 million based on the per share closing price as of April 9, 2009 quoted on the FINRA Over-the-Counter Bulletin Board for the registrant’s common stock, which was $0.20.

There were 60,430,047 shares of the registrant’s common stock, $.001 par value per share outstanding at April 10, 2009.

The Registrant is filing this Amendment No. 2 on Form 10-K/A (this “Abbreviated Amendment”) to amend its Annual Report on Form 10-K for the year ended August 31, 2008, as filed with the Securities and Exchange Commission on October 30, 2008 (“Original Filing Date”) and as amended on December 23, 2008 (the “Original Filing”). This Abbreviated Amendment contains (and amends) only the cover page, this explanatory note, Item 9A(T), the Signature Page and Exhibits 31.1 and 31.2. The purpose of this Abbreviated Amendment is to respond to comments received from the Securities and Exchange Commission and to clarify Item 9A(T) and correct the deficiency in Exhibits 31.1 and 31.2 as originally filed. The Original Filing is hereby superseded and amended only as specially set forth herein and this Abbreviated Amendment does not amend any other information previously filed in the Original Filing. Except as otherwise described herein, the Original Filing continues to speak as of the Original Filing Date.

As of August 31, 2008, we performed an evaluation of the effectiveness of our disclosure controls and procedures that are designed to ensure that the material financial and non-financial information required to be disclosed in our annual report and filed with the SEC is recorded, processed, summarized and reported timely within the time period specified in the SEC’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by an issuer in the reports that it files or submits under the Securities Act, of 1933 as amended, is accumulated and communicated to the issuer’s management, including its principal executive and principal financial officers, or persons performing similar functions, as appropriate to allow timely decisions regarding required disclosure. Based on our evaluation, our management, including our Chief Executive Officer and Chief Financial Officer, have concluded that our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15(d)-15(e) of the Securities Exchange Act of 1934, as amended) as of August 31, 2008, are effective at such reasonable assurance level.

Our management, under the supervision of our Chief Executive Officer and Chief Financial Officer, is responsible for establishing and maintaining adequate internal control over our financial reporting, as defined in Rules 13a-15(f) and 15(d)-15(f) of the Securities Exchange Act of 1934, as amended. The Company’s internal control over financial reporting is defined as a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. Internal control over financial reporting includes policies and procedures that: (i) pertain to the maintenance of records that in reasonable detail accurately and fairly reflect our transactions and asset dispositions; (ii) provide reasonable assurance that transactions are recorded as necessary to permit the preparation of our financial statements in accordance with generally accepted accounting principles, and that our receipts and expenditures are being made only in accordance with authorizations of our management and directors; and (iii) provide reasonable assurance regarding the prevention or timely detection of unauthorized acquisitions, use or disposition of assets that could have a material effect on our financial statements.

Due to its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projects of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

Under the supervision and with the participation of our management, including our Chief Executive Officer and Chief Financial Officer, we evaluated the effectiveness of our internal control over financial reporting as of August 31, 2008. Based on this evaluation, our management concluded that the Company’s internal controls over financial reporting were effective as of August 31, 2008.

This management report on internal control over financial reporting shall not be deemed to be filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended or otherwise subject to the liabilities of that Section.

This annual report does not include an attestation report of the Company’s registered public accounting firm regarding internal control over financial reporting. Management’s report was not subject to an attestation report of the Company’s registered public accounting firm pursuant to temporary rules of the SEC that permit the Company to provide only management’s report in this annual report.

During the most recent fiscal quarter, there have not been any significant changes in our internal controls over financial reporting or in other factors that have materially affected, or are reasonably likely to materially affect, our internal controls over financial reporting.

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.


	RAPTOR PHARMACEUTICALS CORP.
Dated: April 17, 2009	By:	/s/ Kim R. Tsuchimoto
		Kim R. Tsuchimoto
		Chief Financial Officer, Secretary and Treasurer (Principal Financial Officer and Principal Accounting Officer)

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated:


Signatures		Title	Date

*		Chief Executive Officer and Director	April 17, 2009
Christopher M. Starr, Ph.D.		(Principal Executive Officer)

/s/ Kim R. Tsuchimoto Kim R. Tsuchimoto		Chief Financial Officer, Secretary and Treasurer (Principal Financial Officer and Principal Accounting Officer)	April 17, 2009

*		Director	April 17, 2009
Erich Sager

*		Director	April 17, 2009
Raymond William Anderson

*		Director	April 17, 2009
Richard L. Franklin, M.D., Ph.D.

*By:	/s/ Kim R. Tsuchimoto Kim R. Tsuchimoto Attorney-in-Fact


Securities registered under Section 12(b) of the Act:

Title of each class		Name of each exchange on which registered

N/A		N/A
Securities registered under Section 12(g) of the Act:


Large accelerated filer o		Accelerated filer o		Non-accelerated filer o (Do not check if smaller reporting company)		Smaller reporting company X


X		ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934


o		TRANSITION REPORT UNDER SECTION 13 OR 15(d) OF THE EXCHANGE ACT OF 1934