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

                                  FORM 10-K/A

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

                    FOR THE FISCAL YEAR ENDED JULY 28, 2000
                                       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: 000-28369

                             VA LINUX SYSTEMS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

<TABLE>
<S>                                            <C>
                   DELAWARE                                      77-0399299
       (STATE OR OTHER JURISDICTION OF              (I.R.S. EMPLOYER IDENTIFICATION NO.)
        INCORPORATION OR ORGANIZATION)
</TABLE>

               47071 BAYSIDE PARKWAY, FREMONT, CALIFORNIA, 94538
         (ADDRESS, INCLUDING ZIP CODE, OF PRINCIPAL EXECUTIVE OFFICES)

                                 (510) 687-7000
              (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
                                (TITLE OF CLASS)

     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 10K or any amendment to this
Form 10-K.  [X]

     As of September 30, 2000, there were 52,647,849 shares of the Registrant's
Common Stock outstanding. The aggregate market value of the Common Stock held by
non-affiliates of the Registrant as of September 30, 2000 (based on the closing
price for the Common Stock on the Nasdaq National Market on September 29, 2000)
was approximately $1,563,528,379.

                      DOCUMENTS INCORPORATED BY REFERENCE

     Specified portions of the Registrant's Annual Report to Stockholders for
the fiscal year ended July 28, 2000 are incorporated by reference into Parts II
and III of this Form 10-K. Specified portions of the Registrant's definitive
Proxy Statement to be issued in conjunction with Registrant's Annual Meeting of
Stockholders are incorporated by reference into Part III of this Form 10-K.

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<PAGE>   2

The Registrant hereby amends Item 14 contained in the Registrant's Report on
Form 10-K for the fiscal year ended July 28, 2000 to provide for Exhibit 23.3
Report of Independent Public Accountants on Schedule. Except as set forth in
Item 14 below, no other changes are made to the Registrant's Report on Form 10-K
for the fiscal year ended July 28, 2000.
<PAGE>   3

                                    PART IV

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

(c) EXHIBIT INDEX

<TABLE>
<CAPTION>
EXHIBIT
NUMBER
-------
<C>            <S>
  2.1**        Amended and Restated Agreement and Plan of Reorganization
               between the Registrant, Atlanta Acquisition Corp. and
               Andover.Net, Inc.
   3.1*        Amended and Restated Certificate of Incorporation of the
               Registrant
   3.2*        Bylaws of the Registrant
   4.1*        Specimen Common Stock Certificate
  10.1*        Form of Indemnification Agreement between the Registrant and
               each of its directors and officers
  10.2*        1998 Stock Plan and forms of agreement thereunder
  10.3*        1999 Employee Stock Purchase Plan
  10.4*        1999 Director Option Plan
  10.5*        Sublease between Registrant and Boca Global, Inc.
  10.6*        First Amended and Restated Registration Rights Agreement
               between Registrant and certain holders of preferred stock
  10.7*        Founder's Stock Repurchase Agreement
  10.8*        Manufacturing Agreement between the Registrant and Synnex
               Information Technologies, Inc.
  10.9*        Loan and Security Agreement between Registrant and Comerica
               Bank -- California
 10.10*        Master Subcontracted Maintenance Service Provider Agreement
               between Registrant and DecisionOne Corporation
 10.11*        VA Research Linux IA-64 Porting License Agreement between
               Registrant and Intel Corporation
 10.12*        GNU General Public License, version 2
10.13+***      Master Lease Agreement between Boca Global, Inc. and
               Bordeaux Partners LLC
10.14+*****    Master Lease Agreement between Registrant and Renco
               Investment Company
10.15****      Consent of Linus Torvalds
13.1*****      Annual Report to Stockholders for the Fiscal Year Ended July
               28, 2000
23.1*****      Consent of Arthur Andersen LLP, Independent Public
               Accountants (see page 20)
23.2*****      Consent of IDC
  23.3         Report of Independent Public Accountants on Schedule
24.1*****      Power of Attorney (see signature page)
27.1*****      Financial Data Schedules
</TABLE>

---------------
+      Confidential treatment has been requested by the Registrant as to certain
       portions of this exhibit. The omitted portions have been separately filed
       with the Commission.

*      Incorporated by reference to the corresponding exhibit of Registrant's
       form S-1 and the amendments thereto (Commission registration no.
       333-88687).

**     Incorporated by reference to the corresponding exhibit of Registrant's
       form S-4 and the amendment thereto (Commission registration no.
       333-35704).

***   Incorporated by reference from Exhibit 10.16 of Registrant's form S-1 and
      the amendments thereto (Commission registration no. 333-88687).

****  Incorporated by reference from Exhibit 10.18 of Registrant's Quarterly
      Report on Form 10-Q for the period ended January 28, 2000 filed on March
      13, 2000 (Commission file number 000-28369).

***** Previously filed.

                                        2
<PAGE>   4

                                   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.

Date: November 2, 2000

                                          VA Linux Systems, Inc.

                                          By: /s/   LARRY M. AUGUSTIN
                                            ------------------------------------
                                                     Larry M. Augustin
                                               President and Chief Executive
                                                           Officer

                                        3
<PAGE>   5

                                 EXHIBIT INDEX

<TABLE>
<CAPTION>
EXHIBIT
NUMBER
-------
<C>            <S>
  2.1**        Amended and Restated Agreement and Plan of Reorganization
               between the Registrant, Atlanta Acquisition Corp. and
               Andover.Net, Inc.
   3.1*        Amended and Restated Certificate of Incorporation of the
               Registrant
   3.2*        Bylaws of the Registrant
   4.1*        Specimen Common Stock Certificate
  10.1*        Form of Indemnification Agreement between the Registrant and
               each of its directors and officers
  10.2*        1998 Stock Plan and forms of agreement thereunder
  10.3*        1999 Employee Stock Purchase Plan
  10.4*        1999 Director Option Plan
  10.5*        Sublease between Registrant and Boca Global, Inc.
  10.6*        First Amended and Restated Registration Rights Agreement
               between Registrant and certain holders of preferred stock
  10.7*        Founder's Stock Repurchase Agreement
  10.8*        Manufacturing Agreement between the Registrant and Synnex
               Information Technologies, Inc.
  10.9*        Loan and Security Agreement between Registrant and Comerica
               Bank -- California
 10.10*        Master Subcontracted Maintenance Service Provider Agreement
               between Registrant and DecisionOne Corporation
 10.11*        VA Research Linux IA-64 Porting License Agreement between
               Registrant and Intel Corporation
 10.12*        GNU General Public License, version 2
10.13+***      Master Lease Agreement between Boca Global, Inc. and
               Bordeaux Partners LLC
10.14+*****    Master Lease Agreement between Registrant and Renco
               Investment Company
10.15****      Consent of Linus Torvalds
13.1*****      Annual Report to Stockholders for the Fiscal Year Ended July
               28, 2000
23.1*****      Consent of Arthur Andersen LLP, Independent Public
               Accountants (see page 20)
23.2*****      Consent of IDC
  23.3         Report of Independent Public Accountants on Schedule
24.1*****      Power of Attorney (see signature page)
27.1*****      Financial Data Schedules
</TABLE>

---------------
+      Confidential treatment has been requested by the Registrant as to certain
       portions of this exhibit. The omitted portions have been separately filed
       with the Commission.

*      Incorporated by reference to the corresponding exhibit of Registrant's
       form S-1 and the amendments thereto (Commission registration no.
       333-88687).

**     Incorporated by reference to the corresponding exhibit of Registrant's
       form S-4 and the amendment thereto (Commission registration no.
       333-35704).

***   Incorporated by reference from Exhibit 10.16 of Registrant's form S-1 and
      the amendments thereto (Commission registration no. 333-88687).

****  Incorporated by reference from Exhibit 10.18 of Registrant's Quarterly
      Report on Form 10-Q for the period ended January 28, 2000 filed on March
      13, 2000 (Commission file number 000-28369).

***** Previously filed.

                                        4