EXHIBIT 5.1

                         [COOLEY GODWARD LLP LETTERHEAD]

January 21, 2004

Lynx Therapeutics, Inc.
25861 Industrial Blvd.
Hayward, CA 94545

Ladies and Gentlemen:

         You have requested our opinion with respect to certain matters in
connection with the filing by Lynx Therapeutics, Inc., a Delaware corporation
(the "Company"), of a Registration Statement on Form S-3 (the "Registration
Statement") with the Securities and Exchange Commission covering the offering
for resale of (i) 800,000 shares of the Company's common stock (the "Shares"),
with a par value of $0.01, issued in connection with the Securities Purchase
Agreement dated December 31, 2003, by and between the Company and the Purchasers
listed on the signature pages thereto (the "Purchase Agreement") and (ii) up to
200,000 shares of the Company's common stock (the "Warrant Shares") issuable
upon the exercise of warrants for the purchase of the Company's common stock
(the "Warrants"), issued in connection with the Purchase Agreement.

         In connection with this opinion, we have examined the Registration
Statement, the Company's Amended and Restated Certificate of Incorporation and
Bylaws, as amended, the resolutions adopted by the Board of Directors of the
Company on December 30, 2003, and such other documents, records, certificates,
memoranda and other instruments as we deem necessary as a basis for this
opinion. 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. We have relied upon an officer's certificate confirming
receipt of payment for the Shares upon their original issuance.

         On the basis of the foregoing, and in reliance thereon, we are of the
opinion that the Shares have been validly issued, and are fully paid and
nonassessable, and the Warrant Shares, when issued upon exercise of the Warrants
and payment therefor in accordance with the terms of the Warrants, will be
validly issued, fully paid and nonassessable.

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

Sincerely,

COOLEY GODWARD LLP

By: /s/ James C. Kitch
    --------------------------------
    James C. Kitch