<Page>

________________________________________________________________________________

                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                              -------------------

                                  FORM 10-K/A

                                 AMENDMENT NO. 1

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

                  FOR THE FISCAL YEAR ENDED DECEMBER 31, 2002

                                       OR

[ ]            TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)
                     OF THE SECURITIES EXCHANGE ACT OF 1934

          FOR THE TRANSITION PERIOD FROM ____________ TO ____________

                        COMMISSION FILE NUMBER 000-26534

                              -------------------

                           VION PHARMACEUTICALS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

                              -------------------

<Table>
<S>                                            <C>
                   DELAWARE                                      13-3671221
(STATE OR OTHER JURISDICTION OF INCORPORATION                 (I.R.S. EMPLOYER
               OR ORGANIZATION)                             IDENTIFICATION NO.)

                4 SCIENCE PARK
            NEW HAVEN, CONNECTICUT                                 06511
   (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)                      (ZIP CODE)
</Table>

                              -------------------

       REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE: (203) 498-4210

          SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:
                                      None

          SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:

                                 TITLE OF CLASS

 Common Stock, $0.01 par value (together with associated Common Stock Purchase
                                    Rights)

                              -------------------

    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 [ ]

    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. [x]

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

    The aggregate market value of the common stock held by non-affiliates of the
registrant as of June 28, 2002 was $9,715,029 based on the last sale price for
the common stock on that date as reported by the Nasdaq National Market'r'.

    The number of shares outstanding of the registrant's common stock as of
March 21, 2003 was 28,929,839.

________________________________________________________________________________




<Page>


                                    PART IV

ITEM 15. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K

    (a) 1. Financial Statements

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

<Table>
<Caption>
                                                              PAGE
                                                              ----
<S>                                                           <C>
Report of Independent Auditors..............................   27
Balance Sheet as of December 31, 2002 and 2001..............   28
Statement of Operations for the Years Ended December 31,
  2002, 2001 and 2000 and for the Period from May 1, 1994
  (Inception) Through December 31, 2002.....................   29
Statement of Changes in Shareholders' Equity for the Period
  from May 1, 1994 (Inception) Through December 31, 2002....   30
Statement of Cash Flows for the Years Ended December 31,
  2002, 2001 and 2000 and for the Period from May 1, 1994
  (Inception) Through December 31, 2002.....................   33
Notes to Financial Statements...............................   34
</Table>

       2. Financial Statement Schedules

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

       3. Exhibits

    The exhibits required by this item and included in this report or
incorporated herein by reference are as follows:

<Table>
<Caption>
EXHIBIT NO.                                 DESCRIPTION
-----------                                 -----------
<S>           <C>
    2.1       --    Agreement and Plan of Merger among MelaRx Pharmaceuticals,
                    Inc., OncoRx Research Corp. and OncoRx, Inc. dated as of
                    April 19, 1995(1)
    2.2       --    Certificate of Merger, dated April 20, 1995(1)
    3.1       --    Restated Certificate of Incorporation, as amended(2)
    3.2       --    By-laws, as amended(2)
    3.3       --    Certificate of Amendment to the Certificate of Incorporation
                    of Vion Pharmaceuticals, Inc. dated as of July 26, 2001(13)
    4.1       --    Rights Agreement dated as of October 26, 1998 between Vion
                    Pharmaceuticals, Inc. and American Stock Transfer & Trust
                    Company (includes form of Right Certificate attached as
                    Exhibit A and a Summary of Rights to Purchase Common Shares
                    attached as Exhibit B thereto)(3)
    4.2       --    Revised form of Warrant Agreement by and between Vion
                    Pharmaceuticals, Inc. and Brean Murray & Co., Inc.(4)
    4.3       --    Form of Underwriter's Warrant (included as Exhibit A to
                    Exhibit 4.4 above)(4)
   10.1       --    License Agreement between Yale University and OncoRx, Inc.
                    dated as of August 31, 1994
   10.2       --    Letter Agreement between Yale University and OncoRx, Inc.
                    dated August 19, 1994(1)
   10.3       --    Extension Agreement between Yale University and MelaRx
                    Pharmaceuticals, Inc., dated as of July 1, 1992(1)
   10.4       --    License Agreement between Yale University and OncoRx
                    Corporation dated as of November 15, 1995(17)
   10.5       --    Letter Agreement between Yale University and MelaRx
                    Pharmaceuticals, Inc., dated as of February 2, 1995(1)
   10.6       --    Employment Letter from MelaRx Pharmaceuticals, Inc. to
                    Thomas Mizelle, dated as of July 29, 1994(1)
</Table>

                                       1




<Page>

<Table>
<Caption>
EXHIBIT NO.                                 DESCRIPTION
-----------                                 -----------
<S>          <C>
   10.7       --    Marketing Services Agreement between MelaRx Pharmaceuticals,
                    Inc. and Creative Polymers, Inc. dated as of March 21,
                    1994(1)
   10.8       --    License Agreement between Yale University and OncoRx, Inc.
                    dated as of December 15, 1995(17)
   10.9       --    Lease Agreement between Science Park Development Corporation
                    and Vion Pharmaceuticals, Inc., dated as of February 1,
                    1996(6)
   10.10      --    Option Agreement between the Registrant and PMP, Inc., dated
                    April 27, 1995(1)
   10.11      --    Agreement between MelaRx Pharmaceuticals, Inc. and certain
                    shareholders, dated February 17, 1995(1)
   10.12      --    Consulting and Finder's Agreement between MelaRx
                    Pharmaceuticals, Inc. and Jacob A. Melnick, dated June 4,
                    1992, as amended by Agreement dated February 17, 1995(1)
   10.13      --    Clinical Trials Agreement between Vion Pharmaceuticals, Inc.
                    and the Division of Cancer Treatment and Diagnosis, NCI,
                    dated January 9, 2003(17)
   10.14      --    Letter Agreement between Yale University and OncoRx, Inc.
                    (formerly MelaRx Pharmaceuticals, Inc.), dated July 5,
                    1995(1)
   10.15      --    Lease between Science Park Development Corporation and
                    OncoRx, Inc. dated August 10, 1995(7)
   10.16      --    Master Lease Agreement between Citicorp Leasing, Inc. and
                    OncoRx, Inc. dated September 27, 1995(7)
   10.17      --    Sale and Leaseback Agreement and Master Equipment Lease
                    Agreement between FINOVA Technology Finance, Inc. and Vion
                    Pharmaceuticals, Inc. dated as of October 17, 1996(8)

   10.18      --    Clinical Development Agreement between Vion Pharmaceuticals,
                    Inc., Covance Clinical Research Unit Ltd. and Covance
                    Inc.(9, 15)
   10.19      --    Amendment No. 1 to License Agreement between Yale University
                    and Vion Pharmaceuticals, Inc. (f/k/a OncoRx, Inc.) dated as
                    of June 12, 1997(9)
   10.20      --    Amendment No. 2 to License Agreement between Yale University
                    and Vion Pharmaceuticals, Inc. (f/k/a OncoRx, Inc.) dated as
                    of June 12, 1997(9)
   10.21      --    Collaborative Development and Distribution Agreement between
                    Boehringer Ingelheim International GmbH and Vion
                    Pharmaceuticals, Inc. dated November 24, 1997(6, 15)
   10.22      --    Sale and Leaseback Agreement between FINOVA Technology
                    Finance, Inc. and Vion Pharmaceuticals, Inc. dated as of
                    December 10, 1997(6)
   10.23      --    Amendment No. 5 to a License Agreement between Yale
                    University and Vion Pharmaceuticals, Inc. (f/k/a OncoRx,
                    Inc.) dated as of March 3, 2003(16)
   10.24      --    Amendment No. 3 to a License Agreement between Yale
                    University and Vion Pharmaceuticals, Inc. (f/k/a OncoRx,
                    Inc.) dated as of September 25, 1998(10)
   10.25      --    Form of Severance Agreement between the Company and Bijan
                    Almassian, Terrence W. Doyle, Ivan King, Howard B. Johnson,
                    Thomas E. Klein, Thomas Mizelle, Mario Sznol(11)
   10.26      --    Form of Employment Agreement between the Company and Alan
                    Kessman(4)
   10.27      --    Senior Executive Stock Option Plan(11)
   10.28      --    Separation and Release Agreement between the Company and
                    John Spears, dated April 7, 1999(4)
   10.29      --    Development and License Agreement dated December 1, 1999
                    between the Company and Boehringer Ingelheim International
                    GmbH(12, 15)
   10.30      --    Amendment to Clinical Development Agreement between the
                    Company and Covance Clinical Research Unit Ltd. dated
                    October 27, 1999(12, 15)
   10.31      --    Amendment No. 4 to a License Agreement between Yale
                    University and Vion Pharmaceuticals, Inc. (f/k/a OncoRx,
                    Inc.) dated as of January 31, 2000(13, 15)
   10.32      --    Lease between Science Park Development Corporation and Vion
                    Pharmaceuticals, Inc. dated November 1, 2001(14)
</Table>

                                       2




<Page>

<Table>
<Caption>
EXHIBIT NO.                                 DESCRIPTION
-----------                                 -----------
<S>           <C>
   10.33      --    Vion Pharmaceuticals, Inc. Amended and Restated 1993 Stock
                    Option Plan, as Amended(14)
   21.1       --    Subsidiaries of the Registrant(17)
   23.1       --    Consent of Ernst & Young LLP, Independent Auditors(17)
   24.1       --    Power of Attorney(17)
   99.1       --    CEO Certification Pursuant to 18 U.S.C. Section 1350, as
                    Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of
                    2002
   99.2       --    CFO Certification Pursuant to 18 U.S.C. Section 1350, as
                    Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of
                    2002
</Table>

    -------------

 (1)  Incorporated by reference to the Company's Registration
      Statement on Form SB-2 (File No. 33-93468), effective
      August 14, 1995.
 (2)  Incorporated by reference to the Company's Quarterly Report
      on Form 10-QSB for the quarterly period ended June 30, 1998.
 (3)  Incorporated by reference to the Company's Current Report on
      Form 8-K filed on October 26, 1998.
 (4)  Incorporated by reference to the Company's Registration
      Statement on Form S-1 (File No. 333-83837), effective
      October 26, 1999.
 (5)  Reserved
 (6)  Incorporated by reference to the Company's Annual Report on
      Form 10-KSB for the fiscal year ended December 31, 1997.
 (7)  Incorporated by reference to the Company's Quarterly Report
      on Form 10-QSB for the quarter ended September 30, 1995.
 (8)  Incorporated by reference to the Company's Annual Report on
      Form 10-KSB for the fiscal year ended December 31, 1996.
 (9)  Incorporated by reference to the Company's Quarterly Report
      on Form 10-QSB for the quarter ended June 30, 1997.
(10)  Incorporated by reference to the Company's Annual Report on
      Form 10-KSB for the fiscal year ended December 31, 1998.
(11)  Incorporated by reference to the Company's Quarterly Report
      on Form 10-QSB for the quarter ended March 31, 1999.
(12)  Incorporated by reference to the Company's Annual Report on
      Form 10-KSB for the fiscal year ended December 31, 1999.
(13)  Incorporated by reference to the Company's Quarterly Report
      on Form 10-Q for the quarter ended June 30, 2001.
(14)  Incorporated by reference to the Company's Annual Report on
      Form 10-K for the fiscal year ended December 31, 2001.
(15)  Certain portions of this exhibit have been omitted pursuant
      to an order granting confidential treatment by the
      Securities and Exchange Commission.
(16)  Certain portions of this exhibit have been omitted pursuant
      to a request for an order granting confidential treatment by
      the Securities and Exchange Commission.
(17)  Filed on March 28, 2003 with the Company's Annual Report on Form 10-K
      for the fiscal year ended December 31, 2002.

    (b) Reports on Form 8-K

    The Registrant filed the following reports on Form 8-K during the quarter
ended December 31, 2002:

        1. On October 10, 2002, under Item 5 and Item 7 to announce the Company
    initiated a Phase II trial of Triapine'r' in head and neck cancer.

        2. On October 17, 2002, under Item 5 and Item 7 to announce the Company
    would appeal the Nasdaq Stock Market's determination to delist the Company's
    common stock from the Nasdaq National Market'r'.

                                       3




<Page>


        3. On November 6, 2002, under Item 5 and Item 7 to announce that the
    Drug Development Group of the National Cancer Institute's Division of Cancer
    Treatment and Diagnosis had approved a collaboration for the clinical
    development of Triapine.'r'

        4. On November 7, 2002, under Item 5 and Item 7 to announce the
    Company's results for the third quarter and nine-month period ended
    September 30, 2002.

        5. On November 20, 2002, under Item 5 and Item 7 to announce the Company
    had reported clinical results from a Phase I trial of its anticancer agent
    VNP40101M at the EORTC-NCI-AACR 2002 meeting.

        6. On December 10, 2002, under Item 5 and Item 7 to announce the Company
    had reported clinical data on its anticancer agent Triapine at the American
    Society of Hematology meeting.

        7. On December 18, 2002, under Item 5 and Item 7 to announce initial
    data from testing in human patients of an oral formulation of Triapine.

                                       4




<Page>

                                   SIGNATURES

    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.

Dated: July 18, 2003                      VION PHARMACEUTICALS, INC.

                                     By              /s/ ALAN KESSMAN
                                        ........................................
                                                        ALAN KESSMAN
                                           PRESIDENT AND CHIEF EXECUTIVE OFFICER


                                       5




<Page>

                     CERTIFICATE OF CHIEF EXECUTIVE OFFICER

I, Alan Kessman, President and Chief Executive Officer, certify that:

    1. I have reviewed this amendment to annual report on Form 10-K/A (the
"Amendment to Annual Report") of Vion Pharmaceuticals, Inc.;

    2. Based on my knowledge, this Amendment to Annual Report does not contain
any untrue statement of a material fact or omit to state a material fact
necessary to make the statements made, in light of the circumstances under
which such statements were made, not misleading with respect to the period
covered by this Amendment to Annual Report;

    3. Based on my knowledge, the financial statements, and other financial
information included in this Amendment to Annual Report, fairly present in all
material respects the financial condition, results of operations and cash flows
of the registrant as of, and for, the periods presented in this Amendment to
Annual Report;

    4. The registrant's other certifying officers and I are responsible for
establishing and maintaining disclosure controls and procedures (as defined in
Exchange Act Rules 13a-14 and 15d-14) for the registrant and have:

      a) designed such disclosure controls and procedures to ensure that
      material information relating to the registrant, including its
      consolidated subsidiaries, is made known to us by others within those
      entities, particularly during the period in which this Amendment to
      Annual Report is being prepared; and

      b) evaluated the effectiveness of the registrant's disclosure controls and
      procedures as of a date within 90 days prior to the filing date of this
      Amendment to Annual Report.

    5. The registrant's other certifying officers and I have disclosed, based on
our most recent evaluation, to the registrant's auditors and the audit committee
of registrant's board of directors (or persons performing the equivalent
functions):

      a) all significant deficiencies in the design or operation of internal
      controls which could adversely affect the registrant's ability to record,
      process, summarize and report financial data and have identified for the
      registrant's auditors any material weaknesses in internal controls; and

      b) any fraud, whether or not material, that involves management or other
      employees who have a significant role in the registrant's internal
      controls.

                                                   /s/ ALAN KESSMAN
                                          .....................................
                                                       ALAN KESSMAN
                                          PRESIDENT AND CHIEF EXECUTIVE OFFICER

Date: July 18, 2003

                                       6




<Page>

                     CERTIFICATE OF CHIEF FINANCIAL OFFICER

I, Howard B. Johnson, Vice President, Finance and Chief Financial Officer,
certify that:

    1. I have reviewed this amendment to annual report on Form 10-K/A (the
"Amendment to Annual Report") of Vion Pharmaceuticals, Inc.;

    2. Based on my knowledge, this Amendment to Annual Report does not contain
any untrue statement of a material fact or omit to state a material fact
necessary to make the statements made, in light of the circumstances under
which such statements were made, not misleading with respect to the period
covered by this Amendment to Annual Report;

    3. Based on my knowledge, the financial statements, and other financial
information included in this Amendment to Annual Report, fairly present in all
material respects the financial condition, results of operations and cash flows
of the registrant as of, and for, the periods presented in this Amendment to
Annual Report;

    4. The registrant's other certifying officers and I are responsible for
establishing and maintaining disclosure controls and procedures (as defined in
Exchange Act Rules 13a-14 and 15d-14) for the registrant and have:

      a) designed such disclosure controls and procedures to ensure that
      material information relating to the registrant, including its
      consolidated subsidiaries, is made known to us by others within those
      entities, particularly during the period in which this Amendment to
      Annual Report is being prepared; and

      b) evaluated the effectiveness of the registrant's disclosure controls and
      procedures as of a date within 90 days prior to the filing date of this
      Amendment to Annual Report (the 'Evaluation Date').

    5. The registrant's other certifying officers and I have disclosed, based on
our most recent evaluation, to the registrant's auditors and the audit committee
of registrant's board of directors (or persons performing the equivalent
functions):

      a) all significant deficiencies in the design or operation of internal
      controls which could adversely affect the registrant's ability to record,
      process, summarize and report financial data and have identified for the
      registrant's auditors any material weaknesses in internal controls; and

      b) any fraud, whether or not material, that involves management or other
      employees who have a significant role in the registrant's internal
      controls.

                                            /s/ HOWARD B. JOHNSON
                             ...................................................
                                                HOWARD B. JOHNSON
                             VICE PRESIDENT, FINANCE AND CHIEF FINANCIAL OFFICER

Date: July 18, 2003

                                       7