EXHIBIT 31.2

CERTIFICATE OF CHIEF FINANCIAL OFFICER


I, Louise A. Mawhinney, certify that:

1.   I have reviewed this quarterly report on Form 10-Q of ArQule, Inc.

2.   Based on my knowledge, this report does not contain any untrue statement
     of a material fact or omit to state a material fact necessary to make the
     statements made, in light of the circumstances under which such statements
     were made, not misleading with respect to the period covered by this
     report;

3.   Based on my knowledge, the financial statements, and other financial
     information included in this report fairly present in all material
     respects the financial condition, results of operations and cash flows of
     the registrant as of, and for, the periods presented in this report;

4.   The registrant's other certifying officer and I are responsible for
     establishing and maintaining disclosure controls and procedures (as
     defined in Exchange Act Rules 13a-15(e) and 15d-15(e) for the registrant
     and have:

a)   Designed such disclosure controls and procedures, or caused such
     disclosure controls and procedures to be designed under our supervision,
     to ensure that material information relating to the registrant, including
     its consolidated subsidiaries, is made known to us by others within those
     entities, particularly during the period in which this report is being
     prepared;

b)   [Omitted pursuant to the guidance of Release No. 33-8238 (June 5, 2003).]

c)   Evaluated the effectiveness of the registrant's disclosure controls and
     procedures and presented in this report our conclusions about the
     effectiveness of the disclosure controls and procedures as of the end of
     the period covered by this report based on such evaluation; and

d)   Disclosed in this report any change in the registrant's internal control
     over financial reporting that occurred during the registrant's most recent
     fiscal quarter that has materially affected, or is reasonably likely to
     materially affect, the registrant's internal control over financial
     reporting; and

5.   The registrant's other certifying officer and I have disclosed, based on
     our most recent evaluation of internal control over financial reporting,
     to the registrant's auditors and the audit committee of the registrant's
     board of directors (or persons performing the equivalent functions):




a)   All significant deficiencies and material weaknesses in the design or
     operation of internal control over financial reporting which are
     reasonably likely to adversely affect the registrant's ability to record,
     process, summarize and report financial information; and

b)   Any fraud, whether or not material, that involves management or other
     employees who have a significant role in the registrant's internal control
     over financial reporting.


Date: May 7, 2004

                                     /s/ Louise A. Mawhinney
                                     -------------------------------------------
                                     Louise A. Mawhinney
                                     Vice President, Chief Financial Officer
                                     and Treasurer