<PAGE>

                                                                    Exhibit 99.3


                                  CERTIFICATION

I, Louis R. Woodhill, certify that:

     1.   I have reviewed this quarterly report on Form 10-Q of NEON Systems,
          Inc. for the fiscal quarter ended December 31, 2002;

     2.   Based on my knowledge, this quarterly 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 quarterly report;

     3.   Based on my knowledge, the financial statements, and other financial
          information included in this quarterly 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 quarterly report;

     4.   The registrant's other certifying officers and I are responsible for
          establishing and maintaining disclosure controls and procedures (as
          defined in Exchange Act Rules 13a-14 and 15d-14) for the registrant
          and we have:

             a.  designed such disclosure controls and procedures 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
                 quarterly report is being prepared;

             b.  evaluated the effectiveness of the registrant's disclosure
                 controls and procedures as of a date within 90 days prior to
                 the filing date of this quarterly report (the "Evaluation
                 Date"); and

             c.  presented in this quarterly report our conclusions about the
                 effectiveness of the disclosure controls and procedures based
                 on our evaluation as of the Evaluation Date;

     5.   The registrant's other certifying officers and I have disclosed, based
          on our most recent evaluation, to the registrant's auditors and the
          audit committee of registrant's board of directors (or persons
          performing the equivalent function):

             a.  all significant deficiencies in the design or operation of
                 internal controls which could adversely affect the registrant's
                 ability to record, process, summarize and report financial data
                 and have identified for the registrant's auditors any material
                 weaknesses in internal controls; 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; and

     6.   The registrant's other certifying officers and I have indicated in
          this quarterly report whether or not there were significant changes in
          internal controls or in other factors that could significantly affect
          internal controls subsequent to the date of our most recent
          evaluation, including any corrective actions with regard to
          significant deficiencies and material weaknesses.

/s/ Louis R. Woodhill
---------------------

Louis R. Woodhill

Chief Executive Officer

February 12, 2003

                                       33