Exhibit 16.1

November 10, 2004

Securities and Exchange Commission
Washington, D.C.  20549

Ladies and Gentlemen:

We were previously independent auditors for VaxGen, Inc. and, under the date of
March 8, 2004, we reported on the consolidated financial statements of VaxGen,
Inc. as of and for the years ended December 31, 2003 and 2002. On April 6, 2004,
our appointment as independent auditors was terminated. On July 20, 2004 we
advised the Company that we could no longer continue to be associated with the
Company's 2003 and 2002 financial statements and that our reports on the
Company's 2003 and 2002 financial statements could no longer be relied upon. We
have read VaxGen,Inc.'s statements included under Item 4.01 of its Form 8-K/A
dated April 6, 2004, and we agree with such statements except that we are not in
a position to agree or disagree with VaxGen's statements regarding:

      a.    Whether the Audit Committee of the Board of Directors (the Audit
            Committee) of VaxGen, Inc., as part of its regular review of the
            performance of and its relationship with the independent auditors of
            the Company, considered KPMG LLP and two other independent
            accounting firms to serve as the Company's independent auditors in
            2004.

      b.    Whether the Audit Committee is taking an active role in responding
            to the deficiencies identified by KPMG, including overseeing
            management's implementation of remedial measures.

      c.    Whether the Audit Committee and management have taken action in
            response to the deficiencies in the internal controls of the Company
            identified by KPMG LLP, and whether those actions will address the
            condition identified by KPMG LLP as material weaknesses.

      d.    Whether PricewaterhouseCoopers LLP was consulted on the application
            of accounting principles to a specific transaction, either completed
            or proposed, the type of audit opinion that might be rendered on
            VaxGen, Inc.'s consolidated financial statements or any of the
            reportable events described in the Form 8-K/A.

Very truly yours,

                                                        /s/ KPMG LLP

cc:   Randall L-W. Caudill, Audit Committee Chairman, VaxGen, Inc.
      James M. Cunha, Chief Financial Officer, VaxGen, Inc.