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EXHIBIT 31.1 CERTIFICATION OF CHIEF EXECUTIVE OFFICER
PURSUANT TO SECTION 302
OF THE SARBANES-OXLEY ACT OF 2003 I,
David Mitchell, President 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 Amendment
No. 1 to Form 10-Q for the three months ended June 30, 2004. I certify that: 1.    I
have reviewed this Amendment
No. 1 to Form 10-Q of webMethods, Inc.; 2.    Based on my knowledge, this Amendment
No. 1 to Form 10-Q 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 Amendment
No. 1 to Form 10-Q; 3.    Based on my knowledge, the financial statements, and other financial
information included in this Amendment
No. 1 to Form 10-Q, 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 Amendment
No. 1 to Form 10-Q; 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 Amendment
No. 1 to Form 10-Q is being prepared;(b)
    
    evaluated the effectiveness of the registrants disclosure controls
and procedures and presented in this Amendment
No. 1 to Form 10-Q our conclusions about the
effectiveness of the disclosure controls and procedures as of the end
of the period covered by this Amendment
No. 1 to Form 10-Q based on such evaluation; and(c)
    
    disclosed in this Amendment
No. 1 to Form 10-Q 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 fulfilling the equivalent function): (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:
February 14, 2005
    
    /S/ DAVID MITCHELLName: David MitchellTitle: President and Chief Executive Officer