| x | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|---|-----------------------------------------------------------------------------------------|
|  ̈ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|--------|------------------------------------------------------------------------------------------|
|                                                          |   |                                |
|---------------------------------------------------------------|--------|-------------------------------------|
| Delaware                                                      |   | 86-0883978                          |
| (State or other jurisdiction ofincorporation or organization) |   | (I.R.S. EmployerIdentification No.) |
|                              |   |                                                                                                |         |                                |   |   |
|-----------------------------------|--------|-----------------------------------------------------------------------------------------------------|--------------|-------------------------------------|--------|--------|
| Large accelerated filer |   |  ̈                                                                                              |    | Accelerated filer              |   | x      |
| Non-accelerated filer        |   |  ̈   (Do not check if a smaller reporting company) |    | Smaller reporting company |   |  ̈ |

----

----

|                                                           |   |   |
|----------------------------------------------------------------|--------|--------|
| By: /s/ Christopher M. Starr                                   |   |
| Christopher M. Starr, Ph.D.                                    |
| Chief Executive Officer and Director                           |
| (Principal Executive Officer)                                  |
| Date:  June 19, 2013                                      |
|                                                           |   |
| By: /s/ Georgia Erbez                                          |   |
| Georgia Erbez                                                  |
| Chief Financial Officer, Secretary and Treasurer               |
| (Principal Financial Officer and Principal Accounting Officer) |
| Date:  June 19, 2013                                      |

----

|              |         |
|-------------------|--------------|
| (2)               |    | Plan of acquisition, reorganization, arrangement, liquidation or succession |
|              |         |
| 2.1               |    | Agreement and Plan of Merger and Reorganization, dated as of June 7, 2006, by and among Axonyx Inc., Autobahn Acquisition, Inc. and TorreyPines Therapeutics, Inc. (incorporated by reference to Annex A to Registration Statement No. 333-136018 filed on July 25, 2006). |
|              |         |
| 2.2               |    | Amendment No. 1 to Agreement and Plan of Merger and Reorganization, dated as of August 25, 2006, by and among Axonyx Inc., Autobahn Acquisition, Inc. and TorreyPines Therapeutics, Inc. (incorporated by reference to Annex A to Amendment No. 1 to Registration Statement No. 333-136018 filed on August 25, 2006). |
|              |         |
| 2.3               |    | Agreement and Plan of Merger and Reorganization, dated July 27, 2009, by and among Raptor Pharmaceuticals Corp., TorreyPines Therapeutics, Inc., a Delaware corporation, and ECP Acquisition, Inc., a Delaware corporation (incorporated by reference to Exhibit 2.3 to the Registrant's Current Report on Form 8-K, filed on July 28, 2009). |
|              |         |
| (3)(i), (ii) |    | Articles of incorporation; Bylaws |
|              |         |
| 3.1               |    | Certificate of Incorporation of the Registrant (incorporated by reference to Exhibit 3.1 to the Registrant's Current Report on Form 8-K, filed on October 10, 2006). |
|              |         |
| 3.2               |    | Bylaws of the Registrant (incorporated by reference to Exhibit 3.2 to the Registrant's Current Report on Form 8-K, filed on October 10, 2006). |
|              |         |
| 3.3               |    | Certificate of Amendment filed with the Secretary of State of the State of Nevada effecting an 8-for-1 reverse stock of the Registrant's common stock and changing the name of the Registrant from Axonyx Inc. to TorreyPines Therapeutics, Inc. (incorporated by reference to Exhibit 3.3 to the Registrant's Current Report on Form 8-K, filed on October 10, 2006). |
|              |         |
| 3.4               |    | Articles of Conversion filed with the Secretary of State of the State of Nevada changing the state of incorporation of the Registrant (incorporated by reference to Exhibit 3.4 to the Registrant's Current Report on Form 8-K, filed on October 10, 2006). |
|              |         |
| 3.5               |    | Certificate of Conversion filed with the Secretary of State of the State of Delaware (incorporated by reference to Exhibit 3.5 to the Registrant's Current Report on Form 8-K, filed on October 10, 2006). |
|              |         |
| 3.6               |    | Amendment to Bylaws of the Registrant (incorporated by reference to Exhibit 3.6 to the Registrant's Annual Report on Form 10-K, filed on March 29, 2007). |
|              |         |
| 3.7               |    | Charter Amendment for TorreyPines (incorporated by reference to Exhibit 3.1 to the Registrant's Current Report on Form 8-K, filed on October 9, 2009). |
|              |         |
| 3.8               |    | Certificate of Merger between Raptor Pharmaceuticals Corp., ECP Acquisition, Inc. and TorreyPines Therapeutics, Inc. (incorporated by reference to Exhibit 3.2 to the Registrant's Current Report on Form 8-K, filed on October 9, 2009). |
| 3.9               |         | Amendment to Bylaws of the Registrant (incorporated by reference to Exhibit 3.1 to the Registrant's Current Report on Form 8-K, filed on May 14, 2012). |
|                   |         |   |
|                   | (4)          |    | Instruments defining the rights of security holders, including indentures |
|                   |         |   |
|                   | 4.1          |    | Specimen common stock certificate of the Registrant (incorporated by reference to Exhibit 4.7 to the Registrant's Current Report on Form 8-K, filed on October 9, 2009).  |

----

|             | 4.2    |                                                                                                                                                  | Form of Warrant issued to Oxford Financial and Silicon Valley Bank on September 27, 2005 (incorporated by reference to Exhibit 4.16 to the Registrant's Annual Report on Form 10-K, filed on March 29, 2007).                                                                                                                           |
|-------------|--------|------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|             | 4.3    |                                                                                                                                                  | Form of Warrant issued to Comerica Bank on June 11, 2008 (incorporated by reference to Exhibit 4.1 to the Registrant's Report on Form 8-K, filed on June 17, 2008).                                                                                                                                                                               |
|             | 4.4    |                                                                                                                                                  | Rights Agreement Amendment, dated as of July 27, 2009, to the Rights Agreement dated May 13, 2005 between TorreyPines and American Stock Transfer and Trust Company (replacing The Nevada Agency and Trust Company) (incorporated by reference to Exhibit 2.3 to the Registrant's Current Report on Form 8-K, filed on July 28, 2009).  |
|             | 4.5    |                                                                                                                                                       | Amendment to Rights Agreement, dated August 6, 2010, by and between the Registrant and American Stock Transfer & Trust Company, LLC (incorporated by reference to Exhibit 4.2 to the Registrant's Current Report on Form 8-K, filed on August 10, 2010).                                                                                      |
|             | 4.6*   |                                                                                                                                                  | Warrant to purchase common stock dated December 14, 2007 issued to Flower Ventures, LLC (incorporated by reference to Exhibit 4.1 to Raptor Pharmaceuticals Corp.'s Quarterly Report on Form 10QSB/A, filed on April 15, 2008).                                                                                                                   |
|             | 4.7*   |                                                                                                                                                       | Warrant Agreement Amendment, dated December 17, 2009, between the Registrant and Flower Ventures, LLC (incorporated by reference to Exhibit 4.15 to Registrant's Quarterly Report on Form 10QSB, filed on April 9, 2010).                                                                                                                              |
|             |   |                                                                                                                                                       |                                                                                                                                                                                                                                                                                                                                                   |
|             | 4.8*   |                                                                                                                                                       | Form of Placement Agent Warrant to purchase common stock of Raptor Pharmaceuticals Corp. (incorporated by reference to Exhibit 4.2 to Raptor Pharmaceuticals Corp.'s Current Report on Form 8-K/A, filed on May 28, 2008).                                                                                                                             |
|             |   |                                                                                                                                                       |                                                                                                                                                                                                                                                                                                                                                   |
|             | 4.9*   |                                                                                                                                                       | Form of Placement Agent Warrant to purchase common stock of Raptor Pharmaceuticals Corp. (incorporated by reference to Exhibit 4.2 to Raptor Pharmaceuticals Corp.'s Current Report on Form 8-K, filed on August 25, 2009).                                                                                                                            |
|             |   |                                                                                                                                                       |                                                                                                                                                                                                                                                                                                                                                   |
|             | 4.10   |                                                                                                                                                       | Form of Investor Warrants (incorporated by reference to Exhibit 4.1 on Registrant's Current Report on Form 8-K filed on December 18, 2009).                                                                                                                                                                                                  |
|             | 4.11   |                                                                                                                                                       | Form of Investor Warrants (incorporated by reference to Exhibit 4.1 on Registrant's Current Report on Form 8-K filed on August 10, 2010).                                                                                                                                                                                                              |
|             |   |                                                                                                                                                       |                                                                                                                                                                                                                                                                                                                                                   |
|             | 4.12   |                                                                                                                                                       | Placement Agent Warrant (incorporated by reference to Exhibit 4.2 on Registrant's Current Report on Form 8-K filed on August 13, 2010).                                                                                                                                                                                                           |
|             | (10)   |                                                                                                                                                  | Material contracts                                                                                                                                                                                                                                                                                                                                |
|             | 10.1+  |                                                                                                                                                       | Loan Agreement, dated as of December 20, 2012, by and among Registrant, HealthCare Royalty Partners II, L.P. and the Guarantors party thereto (incorporated by reference to Exhibit 10.38 to Registrant's Amendment No. 1 to the Transition Report on Form 10-KT/A filed, on June 19, 2013).                                                           |
| (31)        |   | Section 302 Certification                                                                                                                                  |
|        |   |
| 31.1† |   | Certification of Christopher M. Starr, Ph.D., Chief Executive Officer and Director                                                                         |
|        |   |
| 31.2† |   | Certification of Georgia Erbez, Chief Financial Officer, Secretary and Treasurer                                                                           |
|        |   |
| (32)        |   | Section 906 Certification                                                                                                                                  |
|        |   |
| 32.1† |   | Certification of Christopher M. Starr, Ph.D., Chief Executive Officer and Director, and of Georgia Erbez, Chief Financial Officer, Secretary and Treasurer |

----

|        |   |
|-------------|--------|
| 101**  |   | The following materials from the Raptor Pharmaceutical Corp. Quarterly Report on Form 10-Q for the quarter ended March 31, 2013, formatted in Extensible Business Reporting Language (XBRL): (i) the Condensed Consolidated Balance Sheets; (ii) the Condensed Consolidated Statements of Comprehensive Loss; (iii) the Condensed Consolidated Statement of Stockholders' Equity; (iv) the Condensed Consolidated Statements of Cash Flows; and (v) related notes, tagged as blocks of text. |
| *       | The Raptor Pharmaceuticals Corp. warrants set forth in Exhibits 4.6 - 4.9 has been converted into warrants of the Registrant and the exercise price of such warrants and number of shares of common stock issuable thereunder have been converted as described in Item 1.01 (under the section titled, "Background") of the Registrant's Current Report on Form 8-K, filed on October 5, 2009. |
|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| **      | Furnished herewith and not "filed" for purposes of Section 18 of the Securities Exchange Act of 1934, as amended.                                                                                                                                                                                                                                                                                                  |
| +       | Certain information omitted pursuant to a request for confidential treatment filed with the SEC.                                                                                                                                                                                                                                                                                                                        |
| † | Filed herewith.                                                                                                                                                                                                                                                                                                                                                                                                         |