Exhibit 16.1

April 6, 2004

Securities and Exchange Commission
Washington, D.C.  20549

Ladies and Gentlemen:

We were previously principal accountants 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 principal accountants was terminated. We have read VaxGen,
Inc.'s statements included under Item 4 of its Form 8-K 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.    audit committee and management actions taken in response to the
            deficiencies in the internal controls of the Company identified by
            KPMG LLP;

      b.    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, and;

      c.    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.

Very truly yours,


                                                     /s/ KPMG LLP

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