<PAGE>

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

                                  FORM 10-K/A
                               Amendment No. 1 to

<Table>
<C>          <S>
    [X]      TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)
             OF THE SECURITIES EXCHANGE ACT OF 1934



</Table>

       FOR THE TRANSITION PERIOD FROM JULY 1, 2001 TO DECEMBER 31, 2001.
                             ---------------------

                       COMMISSION FILE NUMBER: 000-21291
                             ---------------------

                          INTROGEN THERAPEUTICS, INC.
             (Exact name of registrant as specified in its charter)

<Table>
<S>                                              <C>
                    DELAWARE                                        74-2704230
        (State or other jurisdiction of                          (I.R.S. Employer
         incorporation or organization)                       Identification Number)

        301 CONGRESS AVENUE, SUITE 1850
                 AUSTIN, TEXAS                                        78701
    (Address of principal executive offices)                        (Zip Code)
</Table>

                                 (512) 708-9310
              (Registrant's telephone number, including area code)

        Securities Registered Pursuant to Section 12(b) of the Act: NONE

Securities Registered Pursuant to Section 12(g) of the Act: COMMON STOCK, $0.001
                                   PAR VALUE

     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 the 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.  [ ]

     The aggregate market value of the voting stock (common stock) held by
non-affiliates of the Registrant, as of December 31, 2001, was approximately
$57.4 million based upon the last sale price reported on the Nasdaq National
Market for December 31, 2001. For purposes of this disclosure, shares of common
stock held by persons who hold more than 5% of the outstanding shares of common
stock and shares held by executive officers and directors of the Registrant have
been excluded because such persons may be deemed to be affiliates. This
determination is not necessarily conclusive.

     As of December 31, 2001, the Registrant had 21,446,363 shares of common
stock, $0.001 par value, issued and outstanding.

                      DOCUMENTS INCORPORATED BY REFERENCE

     Certain information required by Items 10, 11, 12 and 13 of Form 10-K is
incorporated by reference to the Registrant's proxy statement ("2002 Proxy
Statement") for the 2002 Annual Stockholders' Meeting, which will be filed with
the Securities and Exchange Commission within 120 days after the close of the
Registrant's fiscal year ended December 31, 2001.

--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
<PAGE>

EXPLANATORY NOTE

     This Form 10-K/A is being filed as Amendment No. 1 to the Form 10-K of
Introgen Therapeutics, Inc. ("Introgen") filed with the Securities and Exchange
Commission on March 20, 2002 ("Form 10-K") for the purpose of amending Item 9 of
Part II and Item 14 of Part IV of Introgen's Form 10-K.

                                        1
<PAGE>

                                     PART I

     No changes.

                                    PART II

ITEM 9.  CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND
         FINANCIAL DISCLOSURE

     On March 6, 2002, we dismissed Arthur Andersen LLP as our independent
public accountants, effective upon completion of Arthur Andersen LLP's services
in connection with the filing of this Annual Report on Form 10-K for the
six-month transition period ended December 31, 2001.

     Arthur Andersen LLP's reports on our financial statements for each of the
years ended June 30, 2000 and 2001 and for the six-month transition period ended
December 31, 2001 did not contain an adverse opinion or a disclaimer of opinion,
and were not qualified or modified as to uncertainty, audit scope or accounting
principles.

     The decision to change independent public accountants was recommended by
the Audit Committee of our Board of Directors and was approved by our Board of
Directors.

     During each of the two years ended June 30, 2000 and 2001, the six-month
transition period ended December 31, 2001, and through March 20, 2002, there
were no disagreements with Arthur Andersen LLP on any matter of accounting
principles or practices, financial statement disclosure, or auditing scope or
procedures, which disagreements, if not resolved to the satisfaction of Arthur
Andersen LLP, would have caused it to make reference to the subject matter of
the disagreement in connection with its report.

     During each of the two years ended June 30, 2000 and 2001, the six-month
transition period ended December 31, 2001, and through March 20, 2002, Arthur
Andersen LLP did not advise us of any "reportable events" as described in Item
304(a)(1)(v) of Regulation S-K under the Securities Act of 1933, as amended.

     On March 6, 2002, we engaged Ernst & Young LLP as our principal accountants
to audit our financial statements.

     During each of the two years ended June 30, 2000 and 2001, the six-month
transition period ended December 31, 2001, and through March 6, 2002, we did not
consult Ernst & Young LLP on any matters described in Items 304(a)(2)(i) or
304(a)(2)(ii) of Regulation S-K.

                                    PART III

     No changes.

                                    PART IV

ITEM 14.  EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON FORM 8-K

3.  EXHIBITS

     (A) EXHIBITS

<Table>
<Caption>
EXHIBIT
NUMBER                                DESCRIPTION OF DOCUMENT
-------                               -----------------------
<C>           <S>   <C>
 3.1(a)       --    Certificate of Incorporation as currently in effect
 3.1(b)       --    Amendment to Certificate of Incorporation, effective as of
                    December 21, 2001
 3.2(4)       --    Bylaws of Introgen as currently in effect
 4.1(2)       --    Specimen Common Stock Certificate
 4.2(5)       --    Certificate of Designations of Series A Non-Voting
                    Convertible Preferred Stock
</Table>

                                        2
<PAGE>

<Table>
<Caption>
EXHIBIT
NUMBER                                DESCRIPTION OF DOCUMENT
-------                               -----------------------
<C>           <S>   <C>
10.1(1)       --    Form of Indemnification Agreement between Introgen and each
                    of its directors and officers
10.2(1)       --    1995 Stock Plan and form of stock option agreement
                    thereunder
10.3(3)       --    2000 Stock Option Plan and forms of stock option agreements
                    thereunder
10.4(3)       --    2000 Employee Stock Purchase Plan and forms of agreements
                    thereunder
10.5(1)       --    Form of Series C Preferred Stock Purchase Agreement among
                    Introgen and certain investors
10.6(1)       --    Registration Rights Agreement, dated October 31, 1997
10.7(a)(1)    --    Assignment of Leases, dated November 23, 1998, by TMX Realty
                    Corporation and Riverway Bank, and other related agreements
10.7(b)(1)    --    Lease Agreement, dated June 7, 1996, by and between Introgen
                    and Plaza del Oro Business Center
10.7(c)(2)    --    Amendment No. 1 to Lease Agreement, effective as of May 9,
                    1997
10.7(d)(2)    --    Amendment No. 2 to Lease Agreement, effective as of July 31,
                    1998
10.7(e)(2)    --    Amendment No. 3 to Lease Agreement, effective as of June 29,
                    2000
10.8(a)+(1)   --    Patent and Technology License Agreement, effective as of
                    July 20, 1994, by and between the Board of Regents of The
                    University of Texas System, M.D. Anderson Cancer Center and
                    Introgen
10.8(b)+(1)   --    Amendment No. 1 to Patent License Agreement, effective as of
                    September 1, 1996
10.9+(3)      --    Sponsored Research Agreement for Clinical Study, No. CS
                    93-27, dated February 11, 1993, between Introgen and M.D.
                    Anderson, as amended
10.10         --    [RESERVED]
10.11+(3)     --    Sponsored Research Agreement No. SR 93-04, dated February
                    11, 1993 between M.D. Anderson and Introgen, as amended
10.12         --    [RESERVED]
10.13+(3)     --    Sponsored Research Agreement No. SR 96-004 between Introgen
                    and M.D. Anderson, dated January 17, 1996
10.14         --    [RESERVED]
10.15+(3)     --    License Agreement, dated March 29, 1996 between Introgen and
                    SKCC
10.16(1)      --    Consulting Agreement between Introgen and Jack A. Roth,
                    M.D., effective as of October 1, 1994
10.17(1)      --    Consulting Agreement between EJ Financial Enterprises, Inc.
                    and Introgen, effective as of July 1, 1994
10.18(a)(1)   --    Employment Agreement dated as of August 1, 1996 between
                    Introgen and David G. Nance
10.18(b)(1)   --    Amendment No. 1 to Employment Agreement, effective as of
                    August 1, 1998
10.18(c)(1)   --    Amendment No. 2 to Employment Agreement, effective as of
                    February 15, 2000
10.19(1)      --    Service Agreement, effective as of July 1, 1994, between
                    Introgen and Domecq Technologies, Inc.
10.20(a)+(1)  --    Collaboration Agreement (p53 Products), effective as of
                    October 7, 1994, between Introgen and RPR, as amended
10.20(b)+(3)  --    Addendum No. 1 to Collaboration Agreement (p53 Products),
                    dated January 23, 1996, between Introgen and RPR
10.20(c)+(1)  --    1997 Agreement Memorandum, effective as of July 22, 1997,
                    between Introgen and RPR
10.20(d)+(3)  --    Letter Agreement, dated April 19, 1999, from Introgen to RPR
                    regarding manufacturing process for ADVEXIN gene therapy
10.21(a)+(1)  --    Collaboration Agreement (K-ras Products), effective as of
                    October 7, 1994, between Introgen and RPR, as amended
</Table>

                                        3
<PAGE>

<Table>
<Caption>
EXHIBIT
NUMBER                                DESCRIPTION OF DOCUMENT
-------                               -----------------------
<C>           <S>   <C>
10.21(b)(1)   --    Amendment No. 1 to Collaboration Agreement (K-ras Products),
                    effective as of September 27, 1995, between Introgen and RPR
10.22+(3)     --    Collaborative Research and Development Agreement dated
                    October 30, 1998 between Introgen, RPR and NCI
10.23+(1)     --    Non-Exclusive License Agreement, effective as of April 16,
                    1997, by Introgen and Iowa Research Foundation
10.24+(3)     --    Option Agreement, effective as of June 1, 1998, by Introgen
                    and Imperial Cancer Research Technology Limited ("ICRT")
10.25+(3)     --    Option Agreement, effective as of January 1, 1999, by
                    Introgen and ICRT
10.26+(3)     --    Exclusive License Agreement, effective as of July 19, 1999,
                    by Introgen and Corixa Corporation
10.27(a)      --    [RESERVED]
10.27(b)(1)   --    Letter dated January 28, 2000, from Introgen to LXR
                    Biotechnology ("LXR"), notifying LXR of its exercise of its
                    option
10.27(c)+(2)  --    Exclusive License Agreement, effective as of May 16, 2000,
                    by and between Introgen and LXR
10.28+(3)     --    Administrative Services and Management Agreement, effective
                    as of January 1, 1999, by and between Introgen and Gendux,
                    Inc.
10.29+(3)     --    Research and Development Agreement, effective as of January
                    1, 1999, by and between Introgen and Gendux, Inc.
10.30+(3)     --    Delivery Technology License Agreement, effective as of
                    January 1, 1999, by and between Introgen and Gendux, Inc.
10.31+(3)     --    Target Gene License Agreement, effective as of January 1,
                    1999, by and between Introgen and Gendux, Inc.
10.32+(1)     --    Non-Exclusive License Agreement, effective as of August 17,
                    1998, by and between Introgen and National Institutes of
                    Health
10.33         --    [RESERVED]
10.34(2)      --    Master Lease Agreement, effective as of August 4, 1999, by
                    and between Introgen and Finova Capital Corporation
10.35(2)      --    Construction Loan Agreement, effective as of July 24, 2000,
                    by and between Introgen and Compass Bank
10.36+(5)     --    Restated p53 and K-ras Agreement, effective as of June 30,
                    2001, by and among Introgen, Aventis Pharmaceuticals Inc.
                    ("API") and Aventis Pharma S.A. ("Aventis")
10.37(5)      --    P53 Assignment Agreement, effective as of June 30, 2001, by
                    and among Introgen, API and Aventis
10.38(5)      --    K-ras Assignment Agreement, effective as of June 30, 2001,
                    by and among Introgen, API and Aventis
10.39(5)      --    Registration Rights Agreement, effective as of June 30,
                    2001, by and among Introgen, API and RPR
10.40(5)      --    Voting Agreement, effective as of June 30, 2001, by and
                    among Introgen, API and RPR
10.41++       --    Master Services Agreement, effective as of July 9, 2001,
                    between Introgen and PPD Development, LLC
21.1(1)       --    List of subsidiaries of Introgen
23.1          --    Consent of Arthur Andersen LLP, independent public
                    accountants
24.1          --    Power of Attorney (See page 48)
99.1          --    Letter re: Arthur Andersen LLP Representations
</Table>

                                        4
<PAGE>

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

(1) Incorporated by reference to the same-numbered exhibit filed with Introgen's
    Registration Statement on Form S-1 (No. 333-30582) filed with the Securities
    and Exchange Commission on February 17, 2000.

(2) Incorporated by reference to the same-numbered exhibit filed with Amendment
    No. 2 to Introgen's Registration Statement on Form S-1 (No. 333-30582) filed
    with the Securities and Exchange Commission on September 8, 2000.

(3) Incorporated by reference to the same-numbered exhibit filed with Amendment
    No. 3 to Introgen's Registration Statement on Form S-1 (No. 333-30582) filed
    with the Securities and Exchange Commission on October 4, 2000.

(4) Incorporated by reference to the same-numbered exhibit filed with Introgen's
    Quarterly Report on Form 10-Q, for the quarter ended December 31, 2000,
    (File No. 000-21291), filed with the Securities and Exchange Commission on
    February 14, 2001.

(5) Incorporated by reference to the same-numbered exhibit filed with Introgen's
    Annual Report on Form 10-K for the fiscal year ended June 30, 2001 (File No.
    000-21291), filed with the Securities and Exchange Commission on September
    19, 2001.

 +  Confidential treatment has been granted for portions of this exhibit.

 ++ Confidential treatment has been requested for portions of this exhibit.

     (C) EXHIBITS

     See Item 14(3) above.

                                        5
<PAGE>

                                   SIGNATURES

     Pursuant to the requirements of the Securities Exchange Act of 1934, as
amended, the Registrant has duly caused this Amendment No. 1 on Form 10-K/A to
be signed on its behalf by the undersigned thereunto duly authorized in the City
of Austin, Texas, this March 26, 2002.

                                          INTROGEN THERAPEUTICS, INC.

                                          By:      /s/ DAVID G. NANCE
                                            ------------------------------------
                                                       David G. Nance
                                             President, Chief Executive Officer
                                                         and Director
                                               (Principal Executive Officer)

                                          By:  /s/ JAMES W. ALBRECHT, JR.
                                            ------------------------------------
                                                   James W. Albrecht, Jr.
                                                  Chief Financial Officer
                                            (Principal Financial and Accounting
                                                           Officer)

     Pursuant to the requirements of the Securities Exchange Act of 1934, as
amended, this Amendment No. 1 on Form 10-K/A has been signed on behalf of the
Registrant by the following persons in the capacities and on the dates
indicated:

<Table>
<Caption>
                    SIGNATURE                                      TITLE                       DATE
                    ---------                                      -----                       ----
<S>     <C>                                          <C>                                  <C>

                /s/ DAVID G. NANCE                       President, Chief Executive       March 26, 2002
 ------------------------------------------------     Officer, and Director (Principal
                 (David G. Nance)                            Executive Officer)


            /s/ JAMES W. ALBRECHT, JR.               Chief Financial Officer (Principal   March 26, 2002
 ------------------------------------------------    Financial and Accounting Officer)
             (James W. Albrecht, Jr.)


             */s/  JOHN N. KAPOOR, PH.D.             Chairman of the Board and Director   March 26, 2002
 ------------------------------------------------
             (John N. Kapoor, Ph.D.)

        */s/ WILLIAM H. CUNNINGHAM, PH.D.                         Director                March 26, 2002
 ------------------------------------------------
          (William H. Cunningham, Ph.D.)

                 */s/  CHARLES E. LONG                            Director                March 26, 2002
 ------------------------------------------------
                (Charles E. Long)

           */s/  MAHENDRA G. SHAH, PH.D.                          Director                March 26, 2002
 ------------------------------------------------
            (Mahendra G. Shah, Ph.D.)

                   */s/  ELISE T. WANG                            Director                March 26, 2002
 ------------------------------------------------
                 (Elise T. Wang)


 *By:               /s/ DAVID G. NANCE
        -----------------------------------------
                     (David G. Nance)
                     Attorney-in-Fact
</Table>

                                        6
<PAGE>

                                 EXHIBIT INDEX

<Table>
<Caption>
EXHIBIT
NUMBER                           DESCRIPTION OF DOCUMENT
-------                          -----------------------
<C>      <S>   <C>
 10.41+  --    Master Services Agreement, effective as of July 9, 2001,
               between Introgen and PPD Develop-
               ment, LLC
 23.1*   --    Consent of Arthur Andersen LLP, independent public
               accountants
</Table>

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

* Previously filed.

+ Confidential treatment has been requested for portions of this exhibit.