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EXHIBIT 31.1 CERTIFICATION OF CHIEF EXECUTIVE OFFICER PURSUANT TO
SECTION 302
OF THE SARBANES-OXLEY ACT OF 2002 I, Phillip Merrick, Chairman and Chief Executive Officer of webMethods, Inc.,
have executed this certification in connection with the filing with the
Securities and Exchange Commission of the registrants Annual Report on Form
10-K for the fiscal year ended March 31, 2004. I certify that:  1.
    
    I have reviewed this annual report on Form 10-K of webMethods, 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
we 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)
    
    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  (c)
    
    disclosed in this report any change in the registrants
internal controls over financial reporting that occurred during the
registrants most recent fiscal quarter (the registrants fourth
quarter in the case of an annual report) that has materially
affected, or is reasonably likely to materially affect, the
registrants internal controls over financial reporting; and  5.
    
    The registrants other certifying officer and I have disclosed, based on
our most recent evaluation of internal controls over financial reporting,
to the registrants auditors and the audit committee of the registrants
board of directors (or persons fulfilling the equivalent function):  (a)
    
    all significant deficiencies and material weaknesses in the
design or operation of internal controls 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 controls over financial reporting. Date: June 11, 2004 /s/ PHILLIP MERRICKName: Phillip Merrick
Title: Chairman and Chief Executive Officer