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| x ANNUAL REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934.           |
|---------------------------------------------------------------------------------------------|
|                                                                                        |   |
|   For the Fiscal Year Ended December 31, 2012                                          |
|                                                                                        |   |
| o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934. |
|                                                                                        |   |
|   For the transition period from ____________  to  ____________    |

| Delaware                                                            |   | 41-1505029                             |
|---------------------------------------------------------------------|--------|----------------------------------------|
| (State or other jurisdiction of incorporation or organization) |   | (I.R.S. EmployerIdentification Number) |
|                                                                |   |                                   |
| 29 EMMONS DRIVE, SUITE C-10PRINCETON, NJ                            |   |  08540                            |
| (Address of principal executive offices)                            |   | (Zip Code)                             |

|   | (609) 538-8200                                             |   |
|--------|------------------------------------------------------------|--------|
|   | (Registrant’s telephone number, including area code) |   |

| Title of Each Class                           |   | Name of Each Exchange on Which Registered |
|-----------------------------------------------|--------|-------------------------------------------|
|  Common Stock, par value $.001 per share |   | OTCQB                                     |

| Large accelerated filer o | Accelerated filer o | Non-accelerated filer o | Smaller reporting company þ |
|---------------------------|---------------------|-------------------------|----------------------------------|

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| Consolidated Balance Sheets as of December 31, 2012 and 2011                                             | F-2  |
|----------------------------------------------------------------------------------------------------------|------|
| Consolidated Statements of Operations for the Years Ended December 31, 2012 and 2011                     | F-3  |
| Consolidated Statements of Stockholders’ Deficiency for the Years Ended December 31, 2012 and 2011 | F-4  |
| Consolidated Statements of Cash Flows for the Years Ended December 31, 2012 and 2011                     | F-5  |
| Notes to Consolidated Financial Statements                                                               | F-6  |
| Reports of Independent Registered Public Accounting Firms                                                | F-20 |

| 2.1    | Agreement and Plan of Merger, dated May 10, 2006 by and among the Company, Corporate Technology Development, Inc., Enteron Pharmaceuticals, Inc. and CTD Acquisition, Inc. (incorporated by reference to Exhibit 2.1 included in our Registration Statement on Form SB-2 (File No. 333-133975) filed on May 10, 2006). |
|--------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|   |                                                                                                                                                                                                                                                                                                                   |
| 3.1    | Second Amended and Restated Certificate of Incorporation (incorporated by reference to Exhibit 3.1 included in our current report on Form 8-K filed on June 22, 2012).                                                                                                                                            |
|   |                                                                                                                                                                                                                                                                                                                   |
| 3.2    | By-laws (incorporated by reference to Exhibit 3.1 included in our Quarterly Report on Form 10-QSB, as amended, for the fiscal quarter ended June 30, 2003).                                                                                                                                                       |
|   |                                                                                                                                                                                                                                                                                                                   |
| 4.1    | Rights Agreement dated June 22, 2007, between the Company and American Stock Transfer & Trust Company, as Rights Agent (incorporated by reference to Exhibit 4.1 included in our current report on Form 8-K filed on June 22, 2007).                                                                     |
|   |                                                                                                                                                                                                                                                                                                                   |
| 4.2    | Form of Right Certificate (incorporated by reference to Exhibit 4.2 included in our current report on Form 8-K filed on June 22, 2007).                                                                                                                                                                           |
|   |                                                                                                                                                                                                                                                                                                                   |
| 4.3    | Form of Warrant issued to each investor in the January 2009 private placement (incorporated by reference to Exhibit 4.18 included in our Registration Statement on Form S-1 (File No. 333-149239) filed on February 14, 2008).                                                                                         |

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| 4.4    | Form of Warrant issued to each investor in the September 2009 private placement (incorporated by reference to Exhibit 10.2 included in our current report on Form 8-K filed on September 29, 2009).                     |
|--------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|   |                                                                                                                                                                                                                    |
| 4.5    | Warrant dated April 19, 2010, issued to Fusion Capital Fund II, LLC (incorporated by reference to Exhibit 4.10 included in our Post-Effective Amendment to Registration Statement on Form S-1 filed on April 20, 2010). |
|   |                                                                                                                                                                                                                    |
| 4.6    | Form of Common Stock Purchase Warrant issued to each investor in the June 2010 private placement (incorporated by reference to Exhibit 10.2 included in our current report on Form 8-K filed on June 18, 2010).         |
|   |                                                                                                                                                                                                                    |
| 10.1   | Amended and Restated 1995 Omnibus Incentive Plan (incorporated by reference to Exhibit 10.1 included in our Quarterly Report on Form 10-QSB, as amended, for the fiscal quarter ended September 30, 2003). ***          |

| 10.2   | License Agreement between the Company and the University of Texas Southwestern Medical Center (incorporated by reference to Exhibit 10.9 included in our Annual Report on Form 10-KSB filed March 30, 2004, as amended, for the fiscal year ended December 31, 2004). |
|--------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|   |                                                                                                                                                                                                                                                                  |
| 10.3   | License Agreement between the Company and Thomas Jefferson University (incorporated by reference to Exhibit 10.9 included in our Annual Report on Form 10-KSB, as amended, for the fiscal year ended December 31, 2004).                                              |
|   |                                                                                                                                                                                                                                                                  |
| 10.4   | License Agreement between the Company and the University of Texas Medical Branch (incorporated by reference to Exhibit 10.10 included in our Annual Report on Form 10-KSB, as amended, for the fiscal year ended December 31, 2004).                                  |
|   |                                                                                                                                                                                                                                                                  |
| 10.5   | Consulting Agreement between the Company and Lance Simpson of Thomas Jefferson University. (incorporated by reference to Exhibit 10.43 included in our Annual Report on Form 10-KSB as amended for the fiscal year ended December 31, 2002).                          |
|   |                                                                                                                                                                                                                                                                  |
| 10.6   | 2005 Equity Incentive Plan (incorporated by reference to Appendix D to our Proxy Statement filed December 12, 2005). ***                                                                                                                                              |
|   |                                                                                                                                                                                                                                                                  |
| 10.7   | Form S-8 Registration of Stock Options Plan dated December 30, 2005 (incorporated by reference to our registration statement on Form S-8 filed on December 30, 2005).                                                                                                 |
|   |                                                                                                                                                                                                                                                                  |
| 10.8   | Letter of Intent dated January 3, 2007 by and between the Company and Sigma-Tau Pharmaceuticals, Inc. (incorporated by reference to Exhibit 10.1 included in our current report on Form 8-K filed on January 4, 2007).                                           |
|   |                                                                                                                                                                                                                                                                  |
| 10.9   | Letter from Sigma-Tau Pharmaceuticals, Inc. dated February 21, 2007 (incorporated by reference to Exhibit 10.1 included in our current report on Form 8-K filed on February 23, 2007).                                                                                |

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| 10.10       | Letter dated May 3, 2007 between the Company and Sigma-Tau Pharmaceuticals, Inc. (incorporated by reference to Exhibit 10.1 included in our current report on Form 8-K filed on May 4, 2007).                                                                                     |
|-------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|        |                                                                                                                                                                                                                                                                                   |
| 10.11       | Employment Agreement dated December 27, 2007, between Christopher J. Schaber, PhD and the Company (incorporated by reference to Exhibit 10.30 included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2008). ***                                        |
|        |                                                                                                                                                                                                                                                                                   |
| 10.12       | Employment Agreement dated December 27, 2007, between Evan Myrianthopoulos and the Company (incorporated by reference to Exhibit 10.31 included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2008). ***                                               |
|        |                                                                                                                                                                                                                                                                                   |
| 10.13       | Common Stock Purchase Agreement dated February 14, 2008, between the Company and Fusion Capital Fund II, LLC (incorporated by reference to Exhibit 10.35 included in our Registration Statement on Form S-1 filed on February 14, 2008).                                               |
|        |                                                                                                                                                                                                                                                                                   |
| 10.14       | Registration Rights Agreement dated February 14, 2008, between the Company and Fusion Capital Fund II, LLC (incorporated by reference to Exhibit 10.35 included in our Registration Statement on Form S-1 (File No. 333-149239) filed on February 14, 2008).                           |
|        |                                                                                                                                                                                                                                                                                   |
| 10.15       | Letter dated December 1, 2008, between the Company and Sigma-Tau Pharmaceuticals, Inc. (incorporated by reference to Exhibit 10.1 included in our current report on Form 8-K filed on December 1, 2008).                                                                               |
|        |                                                                                                                                                                                                                                                                                   |
| 10.16  | Exclusive License Agreement dated November 24, 1998, between Enteron Pharmaceuticals, Inc. and George B. McDonald, MD and amendments (incorporated by reference to Exhibit 10.42 included in our Registration Statement on Form S-1 (File No. 333-157322) filed on February 13, 2009). |
|        |                                                                                                                                                                                                                                                                                   |
| 10.17  | Collaboration and Supply Agreement dated February 11, 2009, between the Company and Sigma-Tau Pharmaceuticals, Inc. (incorporated by reference to Exhibit 10.43 included in our Registration Statement on Form S-1 (File No. 333-157322) filed on February 13, 2009). †          |

| 10.18  | First Amendment to Common Stock Purchase Agreement dated April 19, 2010 between the Company and Fusion Capital Fund II, LLC (incorporated by reference to Exhibit 10.34 included in our Post-Effective Amendment to Registration Statement on Form S-1 (File No. 333-149239) filed on April 20, 2010). |
|--------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|   |                                                                                                                                                                                                                                                                                                   |
| 10.19  | Amendment to Employment Agreement dated as of January 4, 2011, between The Company and Evan Myrianthopoulos (incorporated by reference to Exhibit 10.1 included in our current report on Form 8-K filed on January 6, 2011). ***                                                                       |

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| 10.20  | Employment Agreement dated as of January 31, 2011 between Kevin Horgan, M.D., and The Company (incorporated by reference to Exhibit 10.1 included in our current report on Form 8-K filed on February 2, 2011). ***                                           |
|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|   |                                                                                                                                                                                                                                                          |
| 10.21  | Employment Agreement dated as of May 31, 2011, between Joseph M. Warusz and The Company (incorporated by reference to Exhibit 10.1 of our current report on Form 8-K filed on May 31, 2011).***                                                               |
|   |                                                                                                                                                                                                                                                          |
| 10.22  | First Amendment to Employment Agreement dated as of July 12, 2011, between The Company and Christopher J. Schaber, PhD (incorporated by reference to Exhibit 10.1 of our current report on Form 8-K filed on July 14, 2011).***                               |
|   |                                                                                                                                                                                                                                                          |
| 10.23  | Second Amendment to Employment Agreement dated as of July 12, 2011, between The Company and Evan Myrianthopoulos (incorporated by reference to Exhibit 10.2 of our current report on Form 8-K filed on July 14, 2011).***                                     |
|   |                                                                                                                                                                                                                                                          |
| 10.24  | Amendment to the Collaboration and Supply Agreement dated July 26, 2011, between Sigma-Tau Pharmaceuticals, Inc. and The Company (incorporated by reference to Exhibit 10.1 of our current report on Form 8-K filed on July 28, 2011).                        |
|   |                                                                                                                                                                                                                                                          |
| 10.25  | Amendment to the Exclusive License Agreement dated as of July 26, 2011, between George McDonald, MD and The Company (incorporated by reference to Exhibit 10.2 of our current report on Form 8-K filed on July 28, 2011).                                     |
|   |                                                                                                                                                                                                                                                          |
| 10.26  | Lease Agreement dated as of February 7, 2012, between CPP II , LLC and The Company (incorporated by reference to Exhibit 10.40 included in our Annual Report on Form 10-K filed March 27, 2012, for the fiscal year ended December 31, 2011).                 |
|   |                                                                                                                                                                                                                                                          |
| 10.27  | Separation Agreement dated February 15, 2012, between Evan Myrianthopoulos and The Company (incorporated by reference to Exhibit 10.28 included in our Registration Statement on Form S-1 (File No. 333-184762) filed on November 5, 2012). ***               |
|   |                                                                                                                                                                                                                                                          |
| 10.28  | First Amendment to Separation Agreement dated July 2, 2012, between Evan Myrianthopoulos and The Company (incorporated by reference to Exhibit 10.29 included in our Registration Statement on Form S-1 (File No. 333-184762) filed on November 5, 2012). *** |
|   |                                                                                                                                                                                                                                                          |
| 10.29  | Amendment No. 2 to the Collaboration and Supply Agreement between the Company, Enteron and Sigma-Tau dated as of December 20, 2012 (incorporated by reference to Exhibit 10.1 of our current report on Form 8-K filed on December 27, 2012). †          |
|   |                                                                                                                                                                                                                                                          |
| 10.30  | Warrant dated December 20, 2012 and issued to Sigma-Tau to purchase 357,069 shares of the Company’s common stock (incorporated by reference to Exhibit 10.2 of our current report on Form 8-K filed on December 27, 2012).                              |
|   |                                                                                                                                                                                                                                                          |
| 10.31  | Warrant dated December 20, 2012 and issued to SINAF S.A. to purchase 87,804 shares of the Company’s common stock (incorporated by reference to Exhibit 10.3 of our current report on Form 8-K filed on December 27, 2012).                              |

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| 10.32  | Amendment to Exclusive License Agreement dated as of December 20, 2012 between Enteron and McDonald (incorporated by reference to Exhibit 10.4 of our current report on Form 8-K filed on December 27, 2012).                   |
|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|   |                                                                                                                                                                                                                            |
| 10.33  | Amendment to Consulting Agreement dated as of December 20, 2012 between Enteron and McDonald (incorporated by reference to Exhibit 10.5 of our current report on Form 8-K filed on December 27, 2012).                          |
|   |                                                                                                                                                                                                                            |
| 10.34  | Warrant dated December 20, 2012 and issued to McDonald to purchase 280,000 shares of the Company’s common stock (incorporated by reference to Exhibit 10.6 of our current report on Form 8-K filed on December 27, 2012). |
|   |                                                                                                                                                                                                                            |
| 21.1   | Subsidiaries of the Company. **                                                                                                                                                                                                 |
|   |                                                                                                                                                                                                                            |
| 23.1   | Consent of EisnerAmper LLP. *                                                                                                                                                                                                   |
| 31.1   | Certification of the Chief Executive Officer pursuant to Exchange Act rule 13(a)-14(a) (under Section 302 of the Sarbanes-Oxley Act of 2002). ** |
|--------|--------------------------------------------------------------------------------------------------------------------------------------------------|
|   |                                                                                                                                             |
| 31.2   | Certification of the Chief Financial Officer pursuant to Exchange Act rule 13(a)-14(a) (under Section 302 of the Sarbanes-Oxley Act of 2002). ** |
|   |                                                                                                                                             |
| 32.1   | Certification of the Chief Executive Officer pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. **                                       |
|   |                                                                                                                                             |
| 32.2   | Certification of the Chief Financial Officer pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. **                                       |

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| *       | Previously filed with the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2012, filed with the Securities and Exchange Commission on February 26, 2013. |
|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| **      | Filed herewith.                                                                                                                                                                           |
| ***     | Indicates management contract or compensatory plan.                                                                                                                                       |
| † | Portions of this exhibit have been omitted pursuant to a request for confidential treatment.                                                                                              |

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|   | SOLIGENIX, INC. |
|--------|-----------------|
|   |            |   |
|   | By:             |  /s/ Christopher J. Schaber |
|   |            | Christopher J. Schaber, PhD |
|   |            | Chief Executive Officer and President |

| Name                             |   | Capacity                                                                         |   | Date          |
|----------------------------------|--------|----------------------------------------------------------------------------------|--------|---------------|
|  /s/ Christopher J. Schaber |   | Chairman of the Board, Chief Executive Officer and President                     |   | June 12, 2013 |
| Christopher J. Schaber, PhD      |   | (principal executive officer)                                                    |   |          |
|                             |   |                                                                             |   |          |
| /s/ Keith L. Brownlie            |   | Director                                                                         |   | June 12, 2013 |
| Keith L. Brownlie, CPA           |   |                                                                             |   |          |
|                             |   |                                                                             |   |          |
| /s/ Gregg A. Lapointe            |   | Director                                                                         |   | June 12, 2013 |
| Gregg A. Lapointe, CPA           |   |                                                                             |   |          |
|                             |   |                                                                             |   |          |
| /s/ Robert J. Rubin              |   | Director                                                                         |   | June 12, 2013 |
| Robert J. Rubin, MD              |   |                                                                             |   |          |
|                             |   |                                                                             |   |          |
| /s/ Jerome Zeldis                |   | Director                                                                         |   | June 12, 2013 |
| Jerome Zeldis, MD, PhD           |   |                                                                             |   |          |
|                             |   |                                                                             |   |          |
| /s/ Joseph M. Warusz             |   | Vice President of Finance, Acting ChiefFinancial Officer and Corporate Secretary |   | June 12, 2013 |
| Joseph M. Warusz, CPA            |   | (principal accounting officer)                                                   |   |          |

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