AURORA BIOSCIENCES CORP
S-8, EX-5.1, 2000-06-21
COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH
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                                                                     EXHIBIT 5.1



                         [COOLEY GODWARD LLP LETTERHEAD]


June 21, 2000



Aurora Biosciences Corporation
11010 Torreyana Road
San Diego, CA  92121

Ladies and Gentlemen:

You have requested our opinion with respect to certain matters in connection
with the filing by Aurora Biosciences Corporation (the "Company") of a
Registration Statement on Form S-8 (the "Registration Statement") with the
Securities and Exchange Commission covering the offering of up to 2,000,000
shares of the Company's Common Stock, $.001 par value (the "Shares"), pursuant
to its 1996 Stock Plan (the "Plan"), as amended as of March 14, 2000.

In connection with this opinion, we have examined the Registration Statement and
related Prospectus, your Certificate of Incorporation and By-laws, as amended,
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.

On the basis of the foregoing, and in reliance thereon, we are of the opinion
that the Shares, when sold and issued in accordance with the Plan as amended on
March 14, 2000, the Registration Statement and related Prospectus, will be
validly issued, fully paid, and nonassessable.

We consent to the filing of this opinion as an exhibit to the Registration
Statement.

Very truly yours,

COOLEY GODWARD LLP


By: /s/ THOMAS A. COLL
   ------------------------------------------
   Thomas A. Coll, Esq.



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