<PAGE>

    As filed with the Securities and Exchange Commission on December 4, 2002
                                                           Registration No. 333-

================================================================================
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                              --------------------
                                    FORM S-8

                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                              --------------------
                               NEON SYSTEMS, INC.
             (Exact name of registrant as specified in its charter)

              DELAWARE                                          76-0345839
    (State or other jurisdiction of                          (I.R.S. Employer
    incorporation or organization)                           Identification No.)

                       14100 SOUTHWEST FREEWAY, SUITE 500
                             SUGAR LAND, TEXAS 77478
                    (Address of Principal Executive Offices)

                              --------------------
                       NEON SYSTEMS, INC. 2002 STOCK PLAN
                  NEON SYSTEMS, INC. 2002 DIRECTOR OPTION PLAN
                           (Full Titles of the Plans)

                                LOUIS R. WOODHILL
                      PRESIDENT AND CHIEF EXECUTIVE OFFICER
                               NEON SYSTEMS, INC.
                       14100 SOUTHWEST FREEWAY, SUITE 500
                             SUGAR LAND, TEXAS 77478
                                 (281) 491-4200
                      (Name, address and telephone number,
                   including area code, of agent for service)

                              --------------------
                                 With copies to:
                              Shelby R. Fike, Esq.
                                Corporate Counsel
                               Neon Systems, Inc.
                       14100 Southwest Freeway, Suite 500
                             Sugar Land, Texas 77478
                                 (281) 491-4200

                              --------------------

                         CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION>
=========================================================================================================================
                                                                                             Proposed
                                                                      Proposed maximum        maximum          Amount of
              Title of securities                 Amount to be        offering price         aggregate       registration
               to be registered                   registered(1)        per share(2)       offering price(2)       fee
-------------------------------------------------------------------------------------------------------------------------
<S>                                              <C>                  <C>                  <C>               <C>
Common Stock to be Issued under the 2002
   Stock Plan..................................  2,292,829 shares           $2.60            $5,961,355        $548.44
-------------------------------------------------------------------------------------------------------------------------
Common Stock to be Issued under the 2002
   Director Option Plan........................    305,000 shares           $2.60            $  793,000        $ 72.96
-------------------------------------------------------------------------------------------------------------------------
TOTAL                                            2,597,829 shares           $2.60            $6,754,355        $621.40
=========================================================================================================================
</TABLE>

__________________
(1)    Pursuant to Rule 416 under the Securities Act of 1933, as amended, this
       registration statement also covers any additional shares of common stock
       of the registrant which become issuable under the antidilution provisions
       of the plans being registered pursuant to the registration statement by
       reason of any stock splits, stock dividends or similar transactions
       effected without the receipt of consideration, which results in an
       increase in the number of the registrant's outstanding shares of common
       stock.
(2)    Estimated in accordance with Rule 457(c) and (h) under the Securities Act
       of 1933, as amended, solely for purposes of calculating the registration
       fee, based on the average of the high and low prices reported on the
       Nasdaq National Market on December 2, 2002.

<PAGE>

                                     PART I

              INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS

         The information specified by Item 1 (Plan Information) and Item 2
(Registrant Information and Employee Plan Annual Information) of Part I of Form
S-8 is omitted from this filing in accordance with the provisions of Rule 428
under the Securities Act of 1933, as amended (the "Securities Act"), and the
introductory Note to Part I of Form S-8.

                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.  Incorporation of Documents by Reference.

         The documents set forth below are incorporated by reference in this
Registration Statement. All documents subsequently filed by NEON Systems, Inc.
("NEON") pursuant to Sections 13(a), 13(c), 14 and 15(d) of the Securities
Exchange Act of 1934, as amended (the "Exchange Act"), prior to the filing of a
post-effective amendment which indicates that all securities offered have been
sold or which deregisters all securities then remaining unsold, shall be deemed
to be incorporated by reference into this Registration Statement and to be a
part hereof from the date of filing of such documents. Any statement contained
in a document incorporated or deemed to be incorporated by reference herein
shall be deemed to be modified or superseded for purposes of this Registration
Statement to the extent a statement contained herein or in any other
subsequently filed document which also is or is deemed to be incorporated by
reference herein modifies or supersedes such statement. Any such statement so
modified or superseded shall not be deemed, except as so modified or superseded,
to constitute a part of this Registration Statement.

         (a)    NEON's annual report on Form 10-K for the year ended March 31,
                2002;

         (b)    All other reports filed with the Securities and Exchange
                Commission ("Commission") pursuant to Section 13(a) or 15(d) of
                the Exchange Act since the end of the fiscal year covered by the
                report described in (a) above; and

         (c)    The description of the Common Stock which is contained in NEON's
                Registration Statement on Form 8-A filed with the Commission on
                March 1, 1999 pursuant to Section 12 of the Exchange Act, and
                all amendments thereto and reports that have been filed for the
                purpose of updating such description.

Item 4.  Description of Securities.

         Not Applicable.

Item 5.  Interests of Named Experts and Counsel.

         Not Applicable.

Item 6.  Indemnification of Directors and Officers.

         Section 145 of the Delaware General Corporation Law (the "DGCL")
provides, in effect, that any person made a party to any action by reason of the
fact that he is or was a director, officer, employee or agent of NEON may and,
in certain cases, must be indemnified by NEON against, in the case of a
non-derivative action, judgments, fines, amounts paid in settlement and
reasonable expenses (including attorney's fees) incurred by him as a result of
such action, and in the case of a derivative action, against expenses (including
attorney's fees), if in either type of action he acted in good faith and in a
manner he reasonably believed to be in or not opposed to the best interests of
NEON. This indemnification does not apply, in a derivative action, to matters as
to which it is adjudged that the director, officer, employee or agent is liable
to NEON, unless upon court order it is determined that, despite such

<PAGE>

adjudication of liability but in view of all the circumstances of the case, he
is fairly and reasonably entitled to indemnity for expenses, and, in a
non-derivative action, to any criminal proceeding in which such person had
reasonable cause to believe his conduct was unlawful.

         Article 15 of NEON's Amended and Restated Certificate of Incorporation
provides that no director of NEON shall be liable to NEON or its stockholders
for monetary damages for breach of fiduciary duty as a director to the fullest
extent permitted by the DGCL.

         Article 16 of NEON's Amended and Restated Certificate of Incorporation
provides that NEON may indemnify to the fullest extent by Delaware law any and
all of its directors and officers, or former directors and officers, or any
person who may have served at NEON's request as a director or officer of another
corporation, partnership, joint venture, trust or other enterprise.

         Reference is made to the form of Indemnification Agreement by and
between NEON and its directors and executive officers filed as Exhibit 10.14 to
NEON's Registration Statement on Form S-1 (File No. 333-69651) declared
effective on March 4, 1999, pursuant to which NEON will be obligated to the
extent permitted by applicable law, to indemnify such directors against all
expenses, judgments, fines and penalties, incurred in connection with the
defense or settlement of any actions brought against them by reason of the fact
that they were directors of NEON or assumed certain responsibilities at the
direction of NEON. NEON has purchased directors' and officers' liability
insurance in order to limit its exposure to liability for indemnification of
directors and officers.

Item 7.  Exemption from Registration Claimed.

         Not Applicable.

Item 8.  Exhibits.

4.1  Amended and Restated Certificate of Incorporation of NEON Systems, Inc.
     (filed with the Commission as Exhibit 3.1 to NEON's Registration Statement
     on Form S-1 (No. 333-69651) filed December 23, 1998 and incorporated herein
     by reference)
4.2  Amendment to the Amended and Restated Certificate of Incorporation of NEON
     Systems, Inc. dated May 15, 2002 (filed with the Commission as Exhibit 3.3
     to NEON's Annual Report on Form 10-K filed June 28, 2002 and incorporated
     herein by reference)
4.3  Amended and Restated Bylaws of NEON Systems, Inc. (filed with the
     Commission as Exhibit 3.2 to NEON's Registration Statement on Form S-1 (No.
     333-69651) filed December 23, 1998 and incorporated herein by reference)
4.4  Specimen Common Stock certificate (filed with the Commission as Exhibit 4.1
     to NEON's Registration Statement on Form S-1/A (No. 333-69651) filed
     February 10, 1999 and incorporated herein by reference)
5.1  Opinion of Vinson & Elkins L.L.P.
23.1 Consent of KPMG LLP 23.2 Consent of Vinson & Elkins L.L.P (included in
     opinion filed as Exhibit 5.1)
24.1 Power of Attorney (included on the signature pages of this Registration
     Statement)
99.1 2002 Stock Plan (filed with the Commission as Exhibit A to NEON's
     definitive proxy statement on Schedule 14A filed on March 5, 2002 and
     incorporated herein by reference)
99.2 2002 Director Option Plan (filed with the Commission as Exhibit B to NEON's
     definitive proxy statement on Schedule 14A filed on March 5, 2002 and
     incorporated herein by reference)

Item 9.  Undertakings.

         NEON hereby undertakes:

         (1)      To file, during any period in which offers or sales are being
                  made, a post-effective amendment to this Registration
                  Statement:

                  (i)      To include any prospectus required by Section
                           10(a)(3) of the Securities Act;

                                      -3-

<PAGE>

              (ii)   To reflect in the prospectus any facts or events arising
                     after the effective date of this Registration Statement (or
                     the most recent post-effective amendment thereof) which,
                     individually or in the aggregate, represent a fundamental
                     change in the information set forth in this Registration
                     Statement;

              (iii)  To include any material information with respect to the
                     plan of distribution not previously disclosed in this
                     Registration Statement or any material change to such
                     information in this Registration Statement;

       provided, however, that the undertakings set forth in paragraphs (1)(i)
       and (1)(ii) above do not apply if the information required to be included
       in a post-effective amendment by those paragraphs is contained in
       periodic reports filed with or furnished to the Commission by NEON
       pursuant to Section 13 or Section 15(d) of the Securities Exchange Act of
       1934 that are incorporated by reference in this Registration Statement;

       (2)    That, for the purpose of determining any liability under the
              Securities Act, each such post-effective amendment shall be deemed
              to be a new registration statement relating to the securities
              offered therein, and the offering of such securities at that time
              shall be deemed to be the initial bona fide offering thereof;

       (3)    To remove from registration by means of a post-effective amendment
              any of the securities being registered which remain unsold at the
              termination of the offering;

       (4)    That, for purposes of determining any liability under the
              Securities Act, each filing of NEON's annual report pursuant to
              Section 13(a) or Section 15(d) of the Exchange Act that is
              incorporated by reference in this Registration Statement shall be
              deemed to be a new registration statement relating to the
              securities offered therein, and the offering of such securities at
              that time shall be deemed to be the initial bona fide offering
              thereof; and

       (5)    Insofar as indemnification for liabilities arising under the
              Securities Act may be permitted to directors, officers and
              controlling persons of NEON pursuant to the foregoing provisions,
              or otherwise, NEON has been advised that in the opinion of the
              Commission such indemnification is against public policy as
              expressed in the Securities Act and is, therefore, unenforceable.
              In the event that a claim for indemnification against such
              liabilities (other than the payment by NEON of expenses incurred
              or paid by a director, officer or controlling person of NEON in
              the successful defense of any action, suit or proceeding) is
              asserted by such director, officer or controlling person in
              connection with the securities being registered, NEON will, unless
              in the opinion of its counsel the matter has been settled by
              controlling precedent, submit to a court of appropriate
              jurisdiction the question of whether such indemnification by it is
              against public policy as expressed in the Securities Act and will
              be governed by the final adjudication of such issue.

                                      -4-

<PAGE>
                                   SIGNATURES

       Pursuant to the requirements of the Securities Act of 1933, the
Registrant certifies that it has reasonable grounds to believe that it meets all
of the requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of Houston, State of Texas, on December 4, 2002.

                                     NEON Systems, Inc.

                                           /s/ Brian D. Helman
                                       By:____________________________
                                          Brian D. Helman
                                          Chief Financial Officer and Secretary

                                POWER OF ATTORNEY

       KNOW ALL MEN AND WOMEN BY THESE PRESENTS, that each person whose
signature appears below hereby constitutes and appoints each of Louis R.
Woodhill and Brian D. Helman, and each of them, his true and lawful
attorneys-in-fact and agents, with full power of substitution and
resubstitution, for him and in his name, place and stead, in any and all
capacities, to sign any and all amendments (including post-effective amendments)
to this Registration Statement, and to file the same, with all exhibits thereto,
and all other documents in connection therewith, with the Securities and
Exchange Commission, granting unto said attorneys-in-fact and agents, and each
of them, full power and authority to do and perform each and every act and thing
requisite and necessary to be done on and about the premises as fully and to all
intents and purposes as he might or could do in person, hereby ratifying and
confirming all that said attorneys-in-fact and agents, or any of them, or their
substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

       Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.

<TABLE>
<CAPTION>
                Signatures                                         Title                               Date
                ----------                                         -----                               ----
<S>                                                 <C>                                             <C>
     /s/ John J. Moores
____________________________________________        Chairman of the Board                           December 4, 2002
         John J. Moores

     /s/ Louis R. Woodhill
____________________________________________        President and Chief Executive Officer           December 4, 2002
         Louis R. Woodhill                          (Principal Executive Officer) and Director

     /s/ Brian D. Helman
____________________________________________        Chief Financial Officer (Principal              December 4, 2002
         Brian D. Helman                            Financial and Accounting Officer) and
                                                    Secretary

     /s/ Peter Schaeffer
____________________________________________        Director                                        December 4, 2002
         Peter Schaeffer

     /s/ Charles E. Noell III
____________________________________________        Director                                        December 4, 2002
         Charles E. Noell III

     /s/ Norris van den Berg
____________________________________________        Director                                        December 4, 2002
         Norris van den Berg

     /s/ Richard Holcomb
____________________________________________        Director                                        December 4, 2002
         Richard Holcomb

     /s/ James R. Woodhill
____________________________________________        Director                                        December 4, 2002
         James R. Woodhill

     /s/ George H. Ellis
____________________________________________        Director                                        December 4, 2002
         George H. Ellis
</TABLE>

                                      -5-

<PAGE>

                                INDEX TO EXHIBITS

   Exhibit
   Number      Exhibit

     4.1      Amended and Restated Certificate of Incorporation of NEON Systems,
              Inc. (filed with the Commission as Exhibit 3.1 to NEON's
              Registration Statement on Form S-1 (No. 333-69651) filed December
              23, 1998 and incorporated herein by reference)
     4.2      Amendment to the Amended and Restated Certificate of Incorporation
              of NEON Systems, Inc. dated May 15, 2002 (filed with the
              Commission as Exhibit 3.3 to NEON's Annual Report on Form 10-K
              filed June 28, 2002 and incorporated herein by reference)
     4.3      Amended and Restated Bylaws of NEON Systems, Inc. (filed with the
              Commission as Exhibit 3.2 to NEON's Registration Statement on Form
              S-1 (No. 333-69651) filed December 23, 1998 and incorporated
              herein by reference)
     4.4      Specimen Common Stock certificate (filed with the Commission as
              Exhibit 4.1 to NEON's Registration Statement on Form S-1/A (No.
              333-69651) filed February 10, 1999 and incorporated herein by
              reference)
     5.1      Opinion of Vinson & Elkins L.L.P.
    23.1      Consent of KPMG LLP
    23.2      Consent of Vinson & Elkins L.L.P. (included in opinion filed as
              Exhibit 5.1)
    24.1      Power of Attorney (included on the signature pages of this
              Registration Statement)
    99.1      2002 Stock Plan (filed with the Commission as Exhibit A to NEON's
              definitive proxy statement on Schedule 14A filed on March 5, 2002
              and incorporated herein by reference)
    99.2      2002 Director Option Plan (filed with the Commission as Exhibit B
              to NEON's definitive proxy statement on Schedule 14A filed on
              March 5, 2002 and incorporated herein by reference)

                                      -6-