**EXHIBIT
        31.1**
 **CERTIFICATIONS**
 I,
        James
        F. Burgess, certify that:
 
 I
        have
        reviewed this quarterly report on Form 10-Q of Mediware Information Systems,
        Inc.;
 
 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;
 
 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;
 
 The
        registrant's other certifying officer(s) 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)) and internal control over financial reporting
        (as
        defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) 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)
        Designed such internal control over financial reporting, or caused such internal
        control over financial reporting to be designed under our supervision, to
        provide reasonable assurance regarding the reliability of financial reporting
        and the preparation of financial statements for external purposes in accordance
        with generally accepted accounting principles;
 
 (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
 
 The
        registrant's other certifying officer(s) 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 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 controls.
   
 Date:
        October 31, 2006
 
 /s/
          James F. Burgess
 James F. Burgess
 Chief Executive Officer