<PAGE>   1
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   FORM 10-K/A

                                 AMENDMENT NO. 1

                                   (MARK ONE)

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

                    FOR THE FISCAL YEAR ENDED JUNE 30, 1999.

                                       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 0-28272

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

<TABLE>
<S>                                                          <C>
           DELAWARE                                              13-3647113
(STATE OR OTHER JURISDICTION OF                               (I.R.S. EMPLOYER
INCORPORATION OR ORGANIZATION)                               IDENTIFICATION NO.)
</TABLE>

                       1201 HARBOR BAY PARKWAY, SUITE 1000
                            ALAMEDA, CALIFORNIA 94502
              (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES AND ZIP CODE)

                                 (510) 748-7150
                         (REGISTRANT'S TELEPHONE NUMBER,
                              INCLUDING AREA CODE)

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

          TITLE OF EACH CLASS NAME OF EACH EXCHANGE ON WHICH REGISTERED

                                      NONE

           SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:
                          COMMON STOCK, $.001 PAR VALUE
                                (TITLE OF CLASS)

Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Sections 13 of 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 any amendments to this Form 10-K/A. [X]

The aggregate market value of the voting stock held by nonaffiliates of the
registrant as of September 21, 1999, was approximately $119,784,849 based upon
the closing sale price of the registrant's Common Stock as reported on the
Nasdaq National Market System on such date. The number of outstanding shares of
the Registrant's Common Stock as of September 21, 1999 was 9,778,355.

<PAGE>   2

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

     (a)  The following documents are filed as part of this Annual Report on
Form 10-K/A:

          (1)  Financial Statements:

               Report of Ernst & Young LLP, Independent Auditors Balance Sheets
               Statements of Operations Statements of Stockholders' Equity
               Statements of Cash Flows Notes to Financial Statements

          (2)  Financial Statements schedules have been omitted from this report
               because the information is provided in the Financial Statements
               or is not applicable.

          (3)  Exhibits

<TABLE>
<CAPTION>
EXHIBIT
NUMBER                                     EXHIBITS
-------                                    --------
<S>            <C>
1.1(1)         Amended and Restated Certificate of Incorporation
3.2(1)         Restated Bylaws of the Registrant
4.1(1)         Specimen Common Stock Certificate
10.2(1, 2)     1993 Stock Option Plan
10.3(9)        1996 Equity Incentive Plan
10.4(1, 2)     Form of Incentive Stock Option Grant
10.5(1, 2)     Form of Nonstatutory Stock Option Grant
10.6(1, 2)     1996 Non-Employee Director Stock Option Plan
10.7(9)        1997 Employee Stock Purchase Plan
10.8(1)        Form of Indemnification Agreement between the Registrant and
               its directors and executive officers
10.9(1)        Form of Common Stock Warrant
10.10(1)       Form of Series A Preferred Stock Warrant
10.11(1)       Form of Series B Preferred Stock Warrant
10.12(1)       Form of Series C Preferred Stock Warrant
10.13(1)       Form of Series D Preferred Stock Warrant
10.19(1)       Form of Bridge Warrant
10.20(1)       License Agreement between the Registrant and Research
               Corporation Technologies, Inc., dated May 15, 1992, as
               amended as of March 21, 1996 and April 26, 1996
10.21(1)       License Agreement between the Registrant and The Johns
               Hopkins University, dated November 23, 1993, as amended as
               of March 21, 1996
10.22(1)       License Agreement between the Registrant and The University
               of Manitoba, dated February 2, 1994
10.23(1)       Form of Underwriters' Warrant
10.24(1)       Lease Agreement between the Registrant and Redding
               Management, Inc., dated September 15, 1992, as amended June
               30, 1995
10.25(1)       Registration Rights Agreement between the Registrant and
               certain stockholders named therein, dated November 1992
10.27(1, 2)    Employment Agreement dated August 10, 1992, between the
               Company and John Monahan.
10.29(8)       Employment Agreement dated August 14, 1996, between the
               Company and Thomas J. Paulson.
10.30(8)       Employment Agreement dated October 23,1996, between the
               Company and Robert M. Mauer.
10.32(8)       Revolving line of credit signed November 22, 1996 with Wells
               Fargo Bank
10.33(8)       Equipment lease dated May 22, 1997 with Transamerica
               Business Credit Corporation
10.34(3)       Common Stock and Warrant Purchase Agreement by and among
               Avigen and certain Purchasers listed on the Schedule of
               Purchasers attached thereto.
10.35(4)       Amendment to Common Stock and Warrant Purchase Agreement by
               and among Avigen and certain Purchasers thereunder dated as
               of September 25, 1998.
10.36(4)       Management Transition Plan
</TABLE>

<PAGE>   3

<TABLE>
<S>            <C>
10.36.1(5)     Form of Common Stock and Warrant Purchase Agreement, dated
               October 30, 1998.
10.37(6)       Form of Common Stock and Warrant Purchase Agreement Date
               February 15, 1999.
10.38(7)(9)    Factor IX patent and know-how exclusive license agreement
               between the Children's Hospital of Philadelphia and Avigen,
               dated May 20, 1999.
10.39(7)       License Agreement between the Registrant and the University
               of Florida Research Foundation, Inc., dated November 13,
               1992, and its First Amendment, dated March 25, 1996
23.1(9)        Consent of Ernst & Young LLP, Independent Auditors
24.1           Power of Attorney (Reference to the signature page herein)
27.1(9)        Financial Data Schedule
</TABLE>

(1)  Filed as an exhibit to the Registrant's Registration Statement on Form S-1
     (No. 333-3220) and incorporated herein by reference.

(2)  Management Contract or Compensation Plan.

(3)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Annual Report on Form 10-K for the year ended June
     30, 1998, as filed with the SEC.

(4)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Quarterly Report on Form 10-Q for the quarter year
     ended September 30, 1998, as filed with the SEC.

(5)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Quarterly Report on Form 10-Q for the quarter year
     ended December 31, 1998.

(6)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Quarterly Report on Form 10-Q for the quarter year
     ended March 31, 1999, as filed with the SEC.

(7)  Confidential treatment has been requested for a portion of this exhibit.

(8)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Annual Report on Form 10-K for the year ended June
     30, 1997, as filed with the SEC.

(9)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Annual Report on Form 10-K for the year ended June
     30, 1999, as filed with the SEC.

     (b)  The Company filed a report on Form 8-K dated May 12, 1999 reporting
          under Item 5 the closing of a private placement.

<PAGE>   4

                                   SIGNATURES

Pursuant to the requirements of Section 13 of 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 on the 10th day of
February, 2000.

                                  AVIGEN, INC.

                                  By: /s/ JOHN MONAHAN
                                      ---------------------------
                                      John Monahan, Ph.D.
                                      President, Chief Executive Officer
                                      and Director

<PAGE>   5




                                  EXHIBIT INDEX

<TABLE>
<CAPTION>
                                                                                             SEQUENTIALLY
EXHIBIT                                                                                        NUMBERED
NUMBER                                    DESCRIPTION OF DOCUMENT                                PAGE
-------                                   -----------------------                            ------------
<S>            <C>                                                                               <C>
1.1(1)         Amended and Restated Certificate of Incorporation
3.2(1)         Restated Bylaws of the Registrant
4.1(1)         Specimen Common Stock Certificate
10.2(1, 2)     1993 Stock Option Plan
10.3(9)        1996 Equity Incentive Plan
10.4(1, 2)     Form of Incentive Stock Option Grant
10.5(1, 2)     Form of Nonstatutory Stock Option Grant
10.6(1, 2)     1996 Non-Employee Director Stock Option Plan
10.7(9)        1997 Employee Stock Purchase Plan
10.8(1)        Form of Indemnification Agreement between the Registrant and
               its directors and executive officers
10.9(1)        Form of Common Stock Warrant
10.10(1)       Form of Series A Preferred Stock Warrant
10.11(1)       Form of Series B Preferred Stock Warrant
10.12(1)       Form of Series C Preferred Stock Warrant
10.13(1)       Form of Series D Preferred Stock Warrant
10.19(1)       Form of Bridge Warrant
10.20(1)       License Agreement between the Registrant and Research
               Corporation Technologies, Inc., dated May 15, 1992, as
               amended as of March 21, 1996 and April 26, 1996
10.21(1)       License Agreement between the Registrant and The Johns
               Hopkins University, dated November 23, 1993, as amended as
               of March 21, 1996
10.22(1)       License Agreement between the Registrant and The University
               of Manitoba, dated February 2, 1994
10.23(1)       Form of Underwriters' Warrant
10.24(1)       Lease Agreement between the Registrant and Redding
               Management, Inc., dated September 15, 1992, as amended June
               30, 1995
10.25(1)       Registration Rights Agreement between the Registrant and
               certain stockholders named therein, dated November 1992
10.27(1, 2)    Employment Agreement dated August 10, 1992, between the
               Company and John Monahan.
10.29(8)       Employment Agreement dated August 14, 1996, between the
               Company and Thomas J. Paulson.
10.30(8)       Employment Agreement dated October 23,1996, between the
               Company and Robert M. Mauer.
10.32(8)       Revolving line of credit signed November 22, 1996 with Wells
               Fargo Bank
10.33(8)       Equipment lease dated May 22, 1997 with Transamerica
               Business Credit Corporation
10.34(3)       Common Stock and Warrant Purchase Agreement by and among
               Avigen and certain Purchasers listed on the Schedule of
               Purchasers attached thereto.
10.35(4)       Amendment to Common Stock and Warrant Purchase Agreement by
               and among Avigen and certain Purchasers thereunder dated as
               of September 25, 1998.
10.36(4)       Management Transition Plan
10.36.1(5)     Form of Common Stock and Warrant Purchase Agreement, dated
               October 30, 1998.
10.37(6)       Form of Common Stock and Warrant Purchase Agreement Date
               February 15, 1999.
10.38(7)(9)    Factor IX patent and know-how exclusive license agreement
               between the Children's Hospital of Philadelphia and Avigen,
               dated May 20, 1999.
10.39(7)       License Agreement between the Registrant and the University
               of Florida Research Foundation, Inc., dated November 13,
               1992, and its First Amendment, dated March 25, 1996
</TABLE>

<PAGE>   6

<TABLE>
<CAPTION>
                                                                                             SEQUENTIALLY
EXHIBIT                                                                                        NUMBERED
NUMBER                                    DESCRIPTION OF DOCUMENT                                PAGE
-------                                   -----------------------                            ------------
<S>            <C>                                                                               <C>
23.1(9)        Consent of Ernst & Young LLP, Independent Auditors
24.1           Power of Attorney (Reference to the signature page herein)
27.1(9)        Financial Data Schedule
</TABLE>

(1)  Filed as an exhibit to the Registrant's Registration Statement on Form S-1
     (No. 333-3220) and incorporated herein by reference.

(2)  Management Contract or Compensation Plan.

(3)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Annual Report on Form 10-K for the year ended June
     30, 1998, as filed with the SEC.

(4)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Quarterly Report on Form 10-Q for the quarter year
     ended September 30, 1998, as filed with the SEC.

(5)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Quarterly Report on Form 10-Q for the quarter year
     ended December 31, 1998.

(6)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Quarterly Report on Form 10-Q for the quarter year
     ended March 31, 1999, as filed with the SEC.

(7)  Confidential treatment has been requested for a portion of this exhibit.

(8)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Annual Report on Form 10-K for the year ended June
     30, 1997, as filed with the SEC.

(9)  Incorporated by reference from such document filed with the SEC as an
     exhibit to the Company's Annual Report on Form 10-K for the year ended June
     30, 1999, as filed with the SEC.

     (b)  The Company filed a report on Form 8-K dated May 12, 1999 reporting
          under Item 5 the closing of a private placement.