Exhibit 5.1

                         Cooley Godward LLP [LETTERHEAD]

Cooley Godward LLP [LOGO]

 June 5, 2003

         VaxGen, Inc.
         1000 Marina Boulevard, Suite 200
         Brisbane, California 94005

         Ladies and Gentlemen:

You have requested our opinion with respect to certain matters in connection
with the sale by VaxGen, Inc., a Delaware corporation (the "Company"), of one
million five hundred ninety-one thousand three hundred seven (1,591,307) shares
of the Company's common stock, $0.01 par value (the "Shares"), pursuant to a
Registration Statement on Form S-3 and the related Prospectus and Prospectus
Supplement filed with the Securities and Exchange Commission (the "Commission").
All of the Shares are to be sold by the Company as described in the Registration
Statement and related Prospectus and Prospectus Supplement.

In connection with this opinion, we have examined and relied upon the
Registration Statement and related Prospectus included therein, the Prospectus
Supplement filed with the Commission pursuant to Rule 424 under the Securities
Act of 1933, as amended, the Company's Amended and Restated Certificate of
Incorporation and Bylaws, as currently in effect, and the originals or copies
certified to our satisfaction of such other records, documents, certificates,
memoranda and other instruments as we deem necessary or appropriate to enable us
to render the opinion expressed below. We have assumed the genuineness and
authenticity of all documents submitted to us as originals, the conformity to
originals of all documents submitted to us as copies thereof and the due
execution and delivery of all documents where due execution and delivery are a
prerequisite to the effectiveness thereof.

On the basis of the foregoing, and in reliance thereon, we are of the opinion
that the Shares, when sold in accordance with the Registration Statement and the
related Prospectus and Prospectus Supplement, will be validly issued, fully paid
and nonassessable.

We consent to the reference to our firm under the caption "Legal Matters" in the
Prospectus and the Prospectus Supplement included in the Registration Statement
and to the filing of this opinion as an exhibit to the Registration Statement.

Very truly yours,

         COOLEY GODWARD LLP


         By: /s/ Laura A. Berezin
            --------------------------------
               Laura A. Berezin