EXHIBIT 5.1

                                   ATTORNEYS AT LAW            Broomfield, CO
                                                               720 566-4000
                                   Five Palo Alto Square
                                   3000 El Camino Real         Reston, VA
                                   Palo Alto, CA               703 456-8000
                                   94306-2155
                                   Main    650 843-5000        San Diego, CA
                                   Fax     650 849-7400        858 550-6000

                                   www.cooley.com              San Francisco, CA
                                                               415 693-2000
                                   JAMES C. KITCH
                                   (650) 843-5027
                                   kitchjc@cooley.com

April 2, 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) 788,235 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 March 9, 2004, by and between the Company and the Purchasers
listed on the signature pages thereto (the "Purchase Agreement") and (ii) up to
181,295 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
March 8, 2004, 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.



Lynx Therapeutics, Inc.
April 2, 2004
Page Two

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