UNITEDSTATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C.20549

FORM 10-K/AAmendment No. 2

|        |                                                                                     |
|--------|-------------------------------------------------------------------------------------|
|   | ANNUAL REPORT PURSUANT TOSECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |

For the fiscal year ended December 31, 2003

OR

|        |                                                                                        |
|--------|----------------------------------------------------------------------------------------|
|   | TRANSITIONREPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACTOF 1934 |

For the transition period from               to              

Commission File Number 000-26534

VIONPHARMACEUTICALS, INC.

(Exact nameof registrant as specified in itscharter)

|                                                               |  |                                    |  |  |  |  |
|---------------------------------------------------------------|--|------------------------------------|--|--|--|--|
| Delaware                                                      |  | 13-3671221                         |
| (Stateor other jurisdiction of incorporation or organization) |  | (I.R.S.Employer IdentificationNo.) |
| 4Science ParkNew Haven,Connecticut                            |  | 06511                              |
| (Addressof principal executive offices)                       |  | (ZipCode)                          |
|                                                               |

Registrant's telephonenumber, including area code: **(203) 498-4210**

Securities registered pursuant to Section 12(b) of theAct: None

Securities registered pursuant toSection 12(g) of the Act:Title ofClassCommon Stock, $0.01 par value(together with associated Common Stock Purchase Rights)

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

Indicate bycheck mark if disclosure of delinquent filers pursuant to Item 405 ofRegulation S-K is not contained herein, and will not be contained, tothe best of registrant's knowledge, in definitive proxy orinformation statements incorporated by reference in Part III of thisForm 10-K or any amendment to this Form 10-K. 

Indicate by check mark whether the registrant is anaccelerated filer (as defined in Rule 12b-2 of the Act). Yes    No 

The aggregate market value ofthe common stock held by non-affiliates of the registrant as of June30, 2003 was $47,555,968 based on the last sale price for the commonstock on that date as reported by the Nasdaq SmallCapMarketSM.

The number of shares outstanding ofthe registrant's common stock as of March 24, 2004 was54,832,383.

----

PART IV

ITEM15.    Exhibits, Financial Statement Schedules, and Reports onForm 8-K

**(a) 1.    FinancialStatements**

The following is a list of the FinancialStatements included in Item 8 of Part II of this Report:

|                                                                                                                                                       |  |        |    |        |  |  |
|-------------------------------------------------------------------------------------------------------------------------------------------------------|--|--------|----|--------|--|--|
|                                                                                                                                                  |  | Page   |
| Report of Independent Auditors                                                                                                                        |  |   | 32 |   |
| Balance Sheets as of December 31, 2003 and2002                                                                                                        |  |   | 33 |   |
| Statements of Operations for theYears Ended December 31, 2003, 2002 and 2001 and for the Period fromMay 1, 1994 (Inception) through December 31, 2003 |  |   | 34 |   |
| Statement of Changes in Shareholders' Equity for thePeriod from May 1, 1994 (Inception) Through December 31,2003                                      |  |   | 35 |   |
| Statements of Cash Flows for theYears Ended December 31, 2003, 2002 and 2001 and for the Period fromMay 1, 1994 (Inception) through December 31, 2003 |  |   | 38 |   |
| Notes to FinancialStatements                                                                                                                          |  |   | 39 |   |
|                                                                                                                                                       |

2.    Financial StatementSchedules

Schedules not included herein are omitted becausethey are inapplicable or not required or because the requiredinformation is given in the financial statements and notes thereto.

3.    Exhibits

The exhibits required by this item andincluded in this report or incorporated herein by reference are asfollows:

|            |  |             |  |                                                                                                                                                                                                                                                                            |  |  |  |  |  |  |
|------------|--|-------------|--|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--|--|--|--|--|--|
| ExhibitNo. |  | Description |
| 2.1        |  | —     |  | Agreementand Plan of Merger among MelaRx Pharmaceuticals, Inc., OncoRx ResearchCorp. and OncoRx, Inc. dated as of April 19, 1995(1)                                                                                                                                        |
| 2.2        |  | —     |  | Certificate ofMerger, dated April 20, 1995(1)                                                                                                                                                                                                                              |
| 3.1        |  | —     |  | Restated Certificateof Incorporation, as amended(2)                                                                                                                                                                                                                        |
| 3.2        |  | —     |  | By-laws, as amended(2)                                                                                                                                                                                                                                                     |
| 3.3        |  | —     |  | Certificate ofAmendment to the Certificate of Incorporation of Vion Pharmaceuticals,Inc. dated as of July 26, 2001(13)                                                                                                                                                     |
| 4.1        |  | —     |  | Rights Agreementdated as of October 26, 1998 between Vion Pharmaceuticals, Inc. andAmerican Stock Transfer & Trust Company (includes form of RightCertificate attached as Exhibit A and a Summary of Rights to PurchaseCommon Shares attached as Exhibit B thereto)(3) |
| 4.2        |  | —     |  | Revised form ofWarrant Agreement by and between Vion Pharmaceuticals, Inc. and BreanMurray & Co., Inc.(4)                                                                                                                                                              |
| 4.3        |  | —     |  | Form ofUnderwriter's Warrant (included as Exhibit A to Exhibit 4.2above) (4)                                                                                                                                                                                               |
| 10.1       |  | —     |  | LicenseAgreement between Yale University and OncoRx, Inc. dated as of August31, 1994 (1,16)                                                                                                                                                                                |
| 10.2       |  | —     |  | LetterAgreement between Yale University and OncoRx, Inc. dated August 19,1994 (1)                                                                                                                                                                                          |
| 10.3       |  | —     |  | ExtensionAgreement between Yale University and MelaRx Pharmaceuticals, Inc.,dated as of July 1, 1992 (1)                                                                                                                                                                   |
|            |

1

----

|            |  |             |  |                                                                                                                                                                        |  |  |  |  |  |  |
|------------|--|-------------|--|------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--|--|--|--|--|--|
| ExhibitNo. |  | Description |
| 10.4       |  | —     |  | LicenseAgreement between Yale University and OncoRx Corporation dated as ofNovember 15, 1995 (15)                                                                      |
| 10.5       |  |        |  | LetterAgreement between Yale University and MelaRx Pharmaceuticals, Inc.,dated as of February 2, 1995(1)                                                               |
| 10.6       |  | —     |  | Reserved                                                                                                                                                               |
| 10.7       |  | —     |  | Reserved                                                                                                                                                               |
| 10.8       |  | —     |  | LicenseAgreement between Yale University and OncoRx, Inc. dated as of December15, 1995(15)                                                                             |
| 10.9       |  | —     |  | Reserved                                                                                                                                                               |
| 10.10      |  | —     |  | Reserved                                                                                                                                                               |
| 10.11      |  | —     |  | Reserved                                                                                                                                                               |
| 10.12      |  | —     |  | Consultingand Finder's Agreement between MelaRx Pharmaceuticals, Inc. andJacob A. Melnick, dated June 4, 1992, as amended by Agreement datedFebruary 17, 1995(1)       |
| 10.13      |  | —     |  | Clinical TrialsAgreement between Vion Pharmaceuticals, Inc. and the Division of CancerTreatment and Diagnosis, NCI, dated January 9, 2003(15)                          |
| 10.14      |  | —     |  | Letter Agreementbetween Yale University and OncoRx, Inc. (formerly MelaRxPharmaceuticals, Inc.), dated July 5, 1995(1)                                                 |
| 10.15      |  | —     |  | Reserved                                                                                                                                                               |
| 10.16      |  | —     |  | Reserved                                                                                                                                                               |
| 10.17      |  | —     |  | Saleand Leaseback Agreement and Master Equipment Lease Agreement betweenFINOVA Technology Finance, Inc. and Vion Pharmaceuticals, Inc. dated asof October 17, 1996 (8) |
| 10.18      |  | —     |  | Reserved                                                                                                                                                               |
| 10.19      |  | —     |  | AmendmentNo. 1 to License Agreement between Yale University and VionPharmaceuticals, Inc. (f/k/a OncoRx, Inc.) dated as of June 12, 1997(9)                            |
| 10.20      |  | —     |  | Amendment No. 2 toLicense Agreement between Yale University and Vion Pharmaceuticals,Inc. (f/k/a OncoRx, Inc.) dated as of June 12, 1997(9)                            |
| 10.21      |  | —     |  | CollaborativeDevelopment and Distribution Agreement between Boehringer IngelheimInternational GmbH and Vion Pharmaceuticals, Inc. dated November 24,1997 (6, 23)       |
| 10.22      |  | —     |  | Reserved                                                                                                                                                               |
| 10.23      |  | —     |  | AmendmentNo. 5 to a License Agreement between Yale University and VionPharmaceuticals, Inc. (f/k/a OncoRx, Inc.) dated as of March 3, 2003(16, 23)                     |
| 10.24      |  | —     |  | Amendment No.3 to a License Agreement between Yale University and VionPharmaceuticals, Inc. (f/k/a OncoRx, Inc.) dated as of September 25,1998 (10)                    |
| 10.25      |  | —     |  | Form ofSeverance Agreement between the Company and Terrence W. Doyle, IvanKing, Howard B. Johnson, Mario Sznol, Thomas Mizelle and BijanAlmassian (11)                 |
| 10.26      |  | —     |  | Reserved                                                                                                                                                               |
| 10.27      |  | —     |  | SeniorExecutive Stock Option Plan (11)                                                                                                                                 |
|            |

2

----

|            |  |             |  |                                                                                                                                                                                                                                                                                                        |  |  |  |  |  |  |
|------------|--|-------------|--|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--|--|--|--|--|--|
| ExhibitNo. |  | Description |
| 10.28      |  | —     |  | Reserved                                                                                                                                                                                                                                                                                               |
| 10.29      |  | —     |  | Development and License Agreement dated December 1,1999 between the Company and Boehringer Ingelheim International GmbH(12, 23)                                                                                                                                                                        |
| 10.30      |  | —     |  | Reserved                                                                                                                                                                                                                                                                                               |
| 10.31      |  | —     |  | Amendment No. 4 to a License Agreement between YaleUniversity and Vion Pharmaceuticals, Inc. (f/k/a OncoRx, Inc.) dated asof January 31, 2000 (13, 23)                                                                                                                                                 |
| 10.32      |  | —     |  | Lease between Science Park Development Corporationand Vion Pharmaceuticals, Inc. dated November 1, 2001(14)                                                                                                                                                                                            |
| 10.33      |  | —     |  | VionPharmaceuticals, Inc. Amended and Restated 1993 Stock Option Plan, asAmended (14)                                                                                                                                                                                                                  |
| 10.34      |  | —     |  | Securities Purchase Agreement as of June 19, 2003(17)                                                                                                                                                                                                                                                  |
| 10.35      |  | —     |  | RegistrationRights Agreement as of June 19, 2003 (17)                                                                                                                                                                                                                                                  |
| 10.36      |  | —     |  | Form of Warrant (17)                                                                                                                                                                                                                                                                                   |
| 10.37      |  | —     |  | Securities Purchase Agreement as of September 8,2003 (18)                                                                                                                                                                                                                                              |
| 10.38      |  | —     |  | Registration Rights Agreement as of September 8,2003 (18)                                                                                                                                                                                                                                              |
| 10.39      |  | —     |  | Form ofWarrant (18)                                                                                                                                                                                                                                                                                    |
| 10.40      |  | —     |  | ResearchServices Agreement between Vion Pharmaceuticals, Inc. and Eli Lilly andCompany as of September 8, 2003 (19,23)                                                                                                                                                                                 |
| 10.41      |  | —     |  | License Agreement between Vion Pharmaceuticals,Inc. and Beijing Pason Pharmaceuticals, Inc. dated September 12, 2003(19, 23)                                                                                                                                                                           |
| 10.42      |  | —     |  | EmploymentAgreement between Vion Pharmaceuticals, Inc. and Alan Kessman dated asof November 3, 2003 (19)                                                                                                                                                                                               |
| 10.43      |  | —     |  | Research Collaboration and Option Agreement with agroup of inventors from the Institute of Pharmacy and the Institute ofMedical Chemistry and Biochemistry at the University of Innsbruck, andAustria Wirtschaftsservice Gesellschaft m.b.H. and VionPharmaceuticals, Inc. dated November 24, 2003(24) |
| 10.44      |  | —     |  | SecuritiesPurchase Agreement as of February 9, 2004(20)                                                                                                                                                                                                                                                |
| 10.45      |  | —     |  | RegistrationRights Agreement as of February 9, 2004(20)                                                                                                                                                                                                                                                |
| 10.46      |  | —     |  | Form of Warrant(20)                                                                                                                                                                                                                                                                                    |
| 10.47      |  | —     |  | LicenseAgreement between Johnson & Johnson Consumer Companies, Inc. andVion Pharmaceuticals, Inc. dated March 1, 2004 (21,24)                                                                                                                                                                      |
| 21.1       |  | —     |  | Subsidiaries of theRegistrant (22)                                                                                                                                                                                                                                                                     |
| 23.1       |  | —     |  | Consentof Ernst & Young LLP, IndependentAuditors                                                                                                                                                                                                                                                   |
| 24.1       |  | —     |  | Power ofAttorney(22)                                                                                                                                                                                                                                                                                   |
| 31.1       |  | —     |  | Certification ofthe Chief Executive Officer pursuant to Section 302 of theSarbanes-Oxley Act of2002                                                                                                                                                                                                    |
| 31.2       |  | —     |  | Certification ofthe Chief Financial Officer pursuant to Section 302 of theSarbanes-Oxley Act of 2002                                                                                                                                                                                                   |
|            |

3

----

|            |  |             |  |                                                                                                     |  |  |  |  |  |  |
|------------|--|-------------|--|-----------------------------------------------------------------------------------------------------|--|--|--|--|--|--|
| ExhibitNo. |  | Description |
| 32.1       |  | —     |  | Certificationof the Chief Executive Officer pursuant to Section 906 of theSarbanes-Oxley Act of2002 |
| 32.2       |  | —     |  | Certification ofthe Chief Financial Officer pursuant to Section 906 of theSarbanes-Oxley Act of2002 |
|            |

|  |
|--|
|  |  |
|  |

|     |                                                                                                                             |
|-----|-----------------------------------------------------------------------------------------------------------------------------|
| (1) | Incorporatedby reference to the Company's Registration Statement on Form SB-2(File No. 33-93468), effective August 14,1995. |

|     |                                                                                                                       |
|-----|-----------------------------------------------------------------------------------------------------------------------|
| (2) | Incorporated by referenceto the Company's Quarterly Report on Form 10-QSB for thequarterly period ended June 30,1998. |

|     |                                                                                                |
|-----|------------------------------------------------------------------------------------------------|
| (3) | Incorporated by referenceto the Company's Current Report on Form 8-K filed on October 26,1998. |

|     |                                                                                                                              |
|-----|------------------------------------------------------------------------------------------------------------------------------|
| (4) | Incorporated by referenceto the Company's Registration Statement on Form S-1 (File No.333-83837), effective October 26,1999. |

|     |          |
|-----|----------|
| (5) | Reserved |

|     |                                                                                                                   |
|-----|-------------------------------------------------------------------------------------------------------------------|
| (6) | Incorporatedby reference to the Company's Annual Report on Form 10-KSB forthe fiscal year ended December 31,1997. |

|     |          |
|-----|----------|
| (7) | Reserved |

|     |                                                                                                                   |
|-----|-------------------------------------------------------------------------------------------------------------------|
| (8) | Incorporatedby reference to the Company's Annual Report on Form 10-KSB forthe fiscal year ended December 31,1996. |

|     |                                                                                                              |
|-----|--------------------------------------------------------------------------------------------------------------|
| (9) | Incorporated by referenceto the Company's Quarterly Report on Form 10-QSB for the quarterended June 30,1997. |

|      |                                                                                                                   |
|------|-------------------------------------------------------------------------------------------------------------------|
| (10) | Incorporated by referenceto the Company's Annual Report on Form 10-KSB for the fiscal yearended December 31,1998. |

|      |                                                                                                               |
|------|---------------------------------------------------------------------------------------------------------------|
| (11) | Incorporated by referenceto the Company's Quarterly Report on Form 10-QSB for the quarterended March 31,1999. |

|      |                                                                                                                   |
|------|-------------------------------------------------------------------------------------------------------------------|
| (12) | Incorporated by referenceto the Company's Annual Report on Form 10-KSB for the fiscal yearended December 31,1999. |

|      |                                                                                                            |
|------|------------------------------------------------------------------------------------------------------------|
| (13) | Incorporated by referenceto the Company's Quarterly Report on Form 10-Q for the quarterended June 30,2001. |

|      |                                                                                                                 |
|------|-----------------------------------------------------------------------------------------------------------------|
| (14) | Incorporated by referenceto the Company's Annual Report on Form 10-K for the fiscal yearended December 31,2001. |

|      |                                                                                                                 |
|------|-----------------------------------------------------------------------------------------------------------------|
| (15) | Incorporated by referenceto the Company's Annual Report on Form 10-K for the fiscal yearended December 31,2002. |

|      |                                                                                                                   |
|------|-------------------------------------------------------------------------------------------------------------------|
| (16) | Incorporated by referenceto the Company's Annual Report on Form 10-K/A for the fiscal yearended December 31,2002. |

|      |                                                                                             |
|------|---------------------------------------------------------------------------------------------|
| (17) | Incorporated by referenceto the Company's Current Report on Form 8-K filed on June 20,2003. |

|      |                                                                                                  |
|------|--------------------------------------------------------------------------------------------------|
| (18) | Incorporated by referenceto the Company's Current Report on Form 8-K filed on September10, 2003. |

|      |                                                                                                                 |
|------|-----------------------------------------------------------------------------------------------------------------|
| (19) | Incorporated byreference to the Company's Quarterly Report on Form 10-Q for thequarter ended September 30,2003. |

|      |                                                                                                 |
|------|-------------------------------------------------------------------------------------------------|
| (20) | Incorporated by referenceto the Company's Current Report on Form 8-K filed on February 11,2004. |

4

----

|      |                                                                                                |
|------|------------------------------------------------------------------------------------------------|
| (21) | Incorporatedby reference to the Company's Current Report on Form 8-K/A filedon March 18, 2004. |

|      |                                                                                                                 |
|------|-----------------------------------------------------------------------------------------------------------------|
| (22) | Filed onMarch 29, 2004 with the Company's Annual Report on Form 10-K forthe fiscal year ended December 31,2003. |

|      |                                                                                                                                                                                                                                               |
|------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (23) | Certain portions of thisexhibit have been omitted pursuant to an order granting confidentialtreatment by the Securities and Exchange Commission. The omittednon-public information has been filed with the Securities and ExchangeCommission. |

|      |                                                                                                                                                                                                                                                             |
|------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (24) | Certain portions ofthis exhibit have been omitted pursuant to a request for an ordergranting confidential treatment by the Securities and ExchangeCommission. The omitted non-public information has been filed with theSecurities and Exchange Commission. |

(b)    Reports onForm 8-K

The Registrant filed the following reports onForm 8-K during the quarter ended December 31,2003:

|          |                                                                                                                                                                                                                                                                                                                                                                                    |
|----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 1.  | On October 22, 2003, underItem 5 and Item 7 to announce the Company had entered into a licenseagreement with Beijing Pason Pharmaceuticals, Inc.("Pason") whereby Pason obtained theexclusive rights to develop, manufacture and market Triapine®anticancer and antiviral uses in the mainland of the People'sRepublic of China, Taiwan, Hong Kong and Macao (the"Territory"). |

|          |                                                                                                                                                                         |
|----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 2.  | On November 12, 2003, under Item 5and Item 7 to announce the Company had received an initial payment of$0.5 million from Pason under the terms of the licenseagreement. |

|          |                                                                                                                                                    |
|----------|----------------------------------------------------------------------------------------------------------------------------------------------------|
| 3.  | On November 13, 2003,under Item 5 and Item 7 to announce the Company's results for thethird quarter and nine-month period ended September 30,2003. |

|          |                                                                                                                                                                                                                                                     |
|----------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 4.  | On December 5, 2003, underItem 5 and Item 7 to announce the Company had entered into a researchcollaboration and option agreement for certain novel anticancercompounds with a group of inventors and Austria WirtschaftsserviceGesellschaft m.b.H. |

|          |                                                                                                                                                                |
|----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 5.  | On December10, 2003, under Item 5 and Item 7 to announce the Company would presenta corporate update at its Annual Meeting of Stockholders on December 9,2003. |

5

----

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of theSecurities Exchange Act of 1934, the registrant has duly caused thisreport to be signed on its behalf by the undersigned, thereunto dulyauthorized, in the City of New Haven, State of Connecticut on May 25,2004.

|        |  |                               |  |                                     |  |  |  |  |  |  |
|--------|--|-------------------------------|--|-------------------------------------|--|--|--|--|--|--|
|   |  | **VIONPHARMACEUTICALS, INC.** |
|   |  | By:                           |  | /s/ Alan Kessman                    |
|   |  |                          |  | Alan KessmanChief Executive Officer |
|        |

Pursuant to therequirements of the Securities Exchange Act of 1934, this report hasbeen signed below by the following persons on behalf of the registrantand in the capacities and on the datesindicated.

|                         |  |                                                                                |  |  |
|-------------------------|--|--------------------------------------------------------------------------------|--|--|
| Signature               |  | Title                                                                          |  |  |
|                         |
| *                       |  | Chairman of theBoard                                                           |  |  |
|                         |
| WilliamR. Miller        |
|                         |
| /s/ AlanKessman         |  | Chief ExecutiveOfficer and Director(Principal ExecutiveOfficer)                |  |  |
|                         |
| Alan Kessman            |
|                         |
| /s/ Howard B.Johnson    |  | President andChief Financial Officer(Principal Financial and AccountingOfficer |  |  |
|                         |
| Howard B. Johnson       |
|                         |
| *                       |  | Director                                                                       |  |  |
|                         |
| StephenK. Carter,M.D.   |
|                         |
| *                       |  | Director                                                                       |  |  |
|                         |
| FrankT.Cary             |
|                         |
| *                       |  | Director                                                                       |  |  |
|                         |
| CharlesK.MacDonald      |
|                         |
| *                       |  | Director                                                                       |  |  |
|                         |
| AlanC. Sartorelli,Ph.D. |
|                         |
| *                       |  | Director                                                                       |  |  |
|                         |
| WalterB.Wriston         |
|                         |

Date:May 25, 2004

|           |                                                                                            |
|-----------|--------------------------------------------------------------------------------------------|
| *By  | /s/ AlanKessman        AlanKessmanAttorney-in-fact |

6

----