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 (the registrant's fourth fiscal quarter in the case of an
    annual report) 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: November 8, 2004

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