<PAGE>   1
     As filed with the Securities and Exchange Commission on April 27, 1999
                              Registration No. 333-


                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549



                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933


                         HEALTH MANAGEMENT SYSTEMS, INC.
             (Exact name of Registrant as specified in its charter)

                                    New York
         (State or other jurisdiction of incorporation or organization)

                                   13-2770433
                     (I.R.S. Employer Identification Number)

                 401 Park Avenue South, New York, New York 10016
                    (Address of Principal Executive Offices)

                         HEALTH MANAGEMENT SYSTEMS, INC.
                       1999 LONG-TERM INCENTIVE STOCK PLAN
                            (Full title of the Plan)



                             Paul J. Kerz, President
                         Health Management Systems, Inc.
                              401 Park Avenue South
                            New York, New York 10016
                     (Name and address of agent for service)

                                  (212)685-4545
          (Telephone number, including area code, of agent for service)



                                   copies to:
                             Bruce S. Coleman, Esq.
                          Coleman, Rhine & Goodwin LLP
                              750 Lexington Avenue
                            New York, New York 10022
                                (212) 317-8880

<PAGE>   2
                         CALCULATION OF REGISTRATION FEE


<TABLE>
<CAPTION>
                                                    Proposed             Proposed
Title of                                            maximum              maximum
securities                     Amount               offering             aggregate            Amount of
to be                          to be                price per            offering             registration
registered                     registered           share (1)            price (1)            fee(2)
------------------------------ ------------------------ --------------- ----------------------- ---------------
<S>                            <C>                      <C>             <C>                           <C>
Common Stock,                  4,751,356(2)             $4.53           $21,523,643                   $-
$.01 par value
------------------------------ ------------------------ --------------- ----------------------- ---------------
</TABLE>

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

(1)      Estimated pursuant to Rules 457(c) and 457(h) under the Securities Act
         of 1933, as amended, and based on the average of the high and low sale
         price reported on the Nasdaq-Amex National Market System of $4.53 on
         April 19, 1999.

(2)      Pursuant to Rule 429(a) under the Securities Act, this Registration
         Statement contains a combined prospectus that relates to Registration
         Statements Nos. 33-65560, 33-76638 and 33-3706 previously filed by the
         Registrant. Pursuant to Rule 429(b) under the Securities Act, all
         4,751,356 shares included herein are being carried forward from
         Registration Statements Nos. 33-65560, 33-76638 and 33-3706. Filing
         fees aggregating $32,198.87 were previously paid with such Registration
         Statements.


         Pursuant to Rule 416 under the Securities Act of 1933, there are also
being registered hereby such additional indeterminate number of shares of Common
Stock as may become issuable by reason of share splits, share dividends and
similar adjustments as set forth in the provisions of the Stock Option Plan and
the respective option agreements entered into thereunder.

<PAGE>   3
                                EXPLANATORY NOTE


         This Registration Statement has been prepared in accordance with the
requirements of Form S-8 to register shares of Common Stock issuable pursuant to
the Registrant's 1999 Long-Term Incentive Stock Plan (the "Plan"). Under cover
of this Form S-8 is a Reoffer Prospectus prepared in accordance with the
requirements of Part I of Form S-3. The S-3 Reoffer Prospectus may be utilized
for reofferings of Common Stock acquired by certain Selling Shareholders through
participation in the Plan.

<PAGE>   4
                                     PART I

              INFORMATION REQUIRED IN THE SECTION 10(A) PROSPECTUS

         Pursuant to Rule 428(b)(1) under the Securities Act of 1933, as amended
(the "Act"), an Information Statement with respect to the Health Management
Systems, Inc. 1999 Long-Term Incentive Stock Plan (the "Plan") will be
distributed to holders of stock options granted under such Plan. The Information
Statement, together with the documents incorporated by reference herein pursuant
to Item 3 of Part II below, taken together, constitute a Section 10(a)
prospectus and the Information Statement is hereby incorporated by reference in
this Registration Statement.

                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

ITEM 3.  INCORPORATION OF DOCUMENTS BY REFERENCE.

         There are hereby incorporated by reference herein the following
documents which have been filed with the Securities and Exchange Commission (the
"Commission"):

         (a) the Registrant's Annual Report on Form 10-K for its fiscal year
ended October 31, 1998, filed with the Commission on January 11, 1999;

         (b) the Registrant's Quarterly Report on Form 10-Q for the quarter
ended January 31, 1999, filed with the Commission on March 17, 1999;

         (c) all other reports filed pursuant to Section 13(a) or 15(d) of the
Securities Exchange Act of 1934, as amended (the "Exchange Act") since the end
of the Registrant's fiscal year ended October 31, 1998; and

         (d) the description of the Registrant's Common Stock contained in the
Registrant's Form 8-A filed with the Commission.

         All documents filed by the Registrant pursuant to Sections 13(a),
13(c), 14 and 15(d) of the Exchange Act after the date of this Registration
Statement and prior to the filing of a post-effective amendment hereto that
indicate that all securities offered have been sold or that deregisters all such
securities then remaining unsold, shall be deemed to be incorporated by
reference herein and to be a part hereof from the date of filing of such
documents.


                                      II-1
<PAGE>   5
         Any statement contained in a document incorporated by reference herein
shall be deemed to be modified or superseded for purposes of this Registration
Statement to the extent that a statement contained herein or in any other
subsequently filed document that also is incorporated or 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.

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 722 of the New York Business Corporation Law (the "BCL")
provides that a corporation may indemnify directors and officers as well as
other employees and individuals against judgments, fines, amounts paid in
settlement and reasonable expenses, including attorneys' fees, in connection
with actions or proceedings, whether civil or criminal (other than an action by
or in the right of the corporation - a "derivative action"), if they acted in
good faith and in a manner they reasonably believed to be in or not opposed to
the best interests of the corporation, and, with respect to any criminal action
or proceeding, had no reasonable cause to believe their conduct was unlawful. A
similar standard is applicable in the case of derivative actions, except that
indemnification only extends to amounts paid in settlement and reasonable
expenses (including attorneys' fees) incurred in connection with the defense or
settlement of such actions, and the statute does not apply in respect of a
threatened action, or a pending action that is settled or otherwise disposed of,
and requires court approval before there can be any indemnification where the
person seeking indemnification has been found liable to the corporation. Section
721 of the BCL provides that Article 7 of the BCL is not exclusive of other
indemnification that may be granted by a corporation's certificate of
incorporation, disinterested director vote, stockholder vote, agreement or
otherwise. Article VIII, Section 7, of the Registrant's by-laws requires the
Registrant to indemnify its officers and directors to the fullest extent
permitted under the BCL.


                                      II-2
<PAGE>   6
         Any amendment to or repeal of the Registrant's certificate of
incorporation or by-laws shall not adversely affect any right or protection of a
director of the Registrant for or with respect to any acts or omissions of such
director occurring prior to such amendment or repeal.

ITEM 7.  EXEMPTION FROM REGISTRATION CLAIMED.

         Not applicable.

ITEM 8.  EXHIBITS.

Exhibit
Number                     Description

4        Health Management Systems, Inc. 1999 Long-Term Incentive Stock Plan.

5        Opinion of Coleman, Rhine & Goodwin LLP with respect to the legality of
         the securities being registered.

23.1     Consent of Coleman, Rhine & Goodwin LLP (included in Exhibit 5).

23.2     Consent of KPMG LLP.

24       Powers of Attorney.

ITEM 9.  UNDERTAKINGS.

         The undersigned Registrant hereby undertakes:

         (a) to file, during any period in which offers or sales are being made,
a post-effective amendment to this Registration Statement to include any
material information with respect to the plan of distribution not previously
disclosed in the Registration Statement or any material change to such
information in the Registration Statement;

         (b) that, for the purpose of determining any liability under the 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; and



                                      II-3
<PAGE>   7
         (c) 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.

         The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the Act, each filing of the Registrant's annual
report pursuant to Section 13(a) or 15(d) of the Exchange Act (and, where
applicable, each filing of an employee benefit plan's annual report pursuant to
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.

         Insofar as indemnification for liabilities arising under the Act may be
permitted to directors, officers and controlling persons of the Registrant
pursuant to the provisions described in Item 6 above, or otherwise, the
Registrant has been advised that in the opinion of the Commission such
indemnification is against public policy as expressed in the Act and is,
therefore, unenforceable. In the event that a claim for indemnification against
such liabilities (other than the payment by the Registrant of expenses incurred
or paid by a director, officer or controlling person of the Registrant 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, the Registrant 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 whether such indemnification by it is against public
policy as expressed in the Act and will be governed by the final adjudication of
such issue.


                                      II-4
<PAGE>   8
REOFFER PROSPECTUS

                         HEALTH MANAGEMENT SYSTEMS, INC.
                              401 PARK AVENUE SOUTH
                            NEW YORK, NEW YORK 10016
                                  (212)685-4545


                                 637,001 Shares

                         Health Management Systems, Inc.

     Our Common Stock is listed on the Nasdaq-Amex National Market System under
the symbol "HMSY". The reported last sale price of the Common Stock on the
Nasdaq-Amex National Market System on April 19, 1999, was $4.44 per share.

     These shares of Common Stock may be issued to our officers, directors and
employees when they exercise stock options and other awards granted to them
under our Long-Term Incentive Stock Plan and our prior Stock Option and
Restricted Stock Purchase Plan. These shareholders may then sell these shares in
the open market or otherwise. We will not receive any part of the proceeds from
these sales.

         The shares have not been approved by the SEC or any state securities
commission, nor have these organizations determined that this prospectus is
accurate or complete. Any representation to the contrary is a criminal offense.

                  The date of this Prospectus is April 27, 1999
<PAGE>   9
                                TABLE OF CONTENTS

Where You Can Find More Information.....................................1

About Health Management Systems, Inc. ("HMS")...........................2

Selling Shareholders....................................................4

Plan of Distribution....................................................5

Validity of the Shares..................................................5

Experts.................................................................5

Other Matters...........................................................6

<PAGE>   10

                       WHERE YOU CAN FIND MORE INFORMATION

         We file annual, quarterly and special reports, proxy statements and
other information with the SEC. You may read and copy any document we file at
the SEC's public reference rooms in Washington, D.C., New York, New York and
Chicago, Illinois. Please call the SEC at 1-800-SEC-0330 for further information
on the public reference rooms. Our SEC filings are also available to the public
from our web site at www.hmsy.com or at the SEC's web site at www.sec.gov.

         The SEC allows us to "incorporate by reference" the information we file
with them, which means that we can disclose important information to you by
referring you to those documents. The information incorporated by reference is
considered to be part of this prospectus, and later information that we file
with the SEC will automatically update and supersede this information. We
incorporate by reference the documents listed below and any future filings made
with the SEC under Sections 13(a), 13(c), 14 or 15(d) of the Securities Exchange
Act of 1934 until the selling shareholders sell all the shares covered by this
prospectus. This prospectus is part of a registration statement we filed with
the SEC (Registration No. 333-____).

         We are incorporating the following documents by reference:

         Annual Report on Form 10-K for the year ended October 31, 1998; and

         Quarterly Report on Form 10-Q for the quarter ended January 31, 1999.

         You may request a copy of these filings, at no cost, by writing or
telephoning us at the following address:

                  Shareholder Services
                  Health Management Systems, Inc.
                  401 Park Avenue South
                  New York, New York 10016
                  (212)685-4545

         You should rely only on the information incorporated by reference or
provided in this prospectus or any supplement. We have not authorized anyone
else to provide you with different information. The selling shareholders will
not make an offer of these shares in any state where the offer is not permitted.
You should not assume that the information in this prospectus or any supplement


                                       1
<PAGE>   11
is accurate as of any date other than the date on the front of those documents.

                                    ABOUT HMS

         HMS furnishes proprietary information management and data processing
products and services to healthcare providers and payors, including government
health service agencies. These services address the various types of data
generated by the interaction of the participants in the healthcare delivery
process: the providers of care, the third-party payors, and the patients.
Through its product and service offerings, the Company acts as an outsourcer of
information management functions addressing the operational, administrative,
financial, and clinical data that result from the rendering of healthcare
services to patients. The Company's product and service offerings benefit its
clients by enhancing revenue (achieved through improved reimbursability,
profitability, and/or collectability), accelerating cash flow, reducing
operating and administrative costs (by supplying advanced information
analytics), and improving decision-making capabilities (via the provision of
useful information).

         Healthcare providers receive payment for services from patients,
third-party payors, or a combination thereof. Third-party payors include
commercial insurance companies, governments or their fiscal agents and
intermediaries, health maintenance organizations, preferred provider
organizations, third-party administrators for self-insured companies, and
managed care companies. Although patients generally retain primary
responsibility for payment for all healthcare services, third-party payors bear
the preponderance of the responsibility for many charges for care. Obtaining
reimbursement from third-party payors has become increasingly difficult because
of frequent changes in reimbursement formulae and contractual requirements for
pre-admission certification and utilization review, and administrative
procedures instituted by third-party payors in an effort to control costs. To be
successful in obtaining payment from third-party payors, hospitals and other
healthcare providers require regulatory knowledge and technical skills to manage
complex data collection, integration, analysis, and accounts receivable
management functions. To ensure that program costs are not greater than
necessary, third-party payors require knowledge and skills analogous to those
required by providers.



                                       2
<PAGE>   12
         Using the operational, financial, administrative, and clinical data
generated as part of the healthcare delivery process, the Company applies
proprietary software and other analytical tools to transform data into valuable
information that clients use to (i) minimize operating and administrative costs
while improving profitability, (ii) measure the quality of care, and (iii)
optimize the outcome of the transfer payment processes linking payors,
providers, and patients. Customers of the Company utilize the Company's products
and services to improve their decision-making and operating capabilities and to
achieve improved operational, administrative, financial, and clinical
performance. The Company believes its customers benefit from the Company's
unique understanding of the healthcare delivery and associated transfer payment
processes, from the perspective of both providers and payors.


                                       3
<PAGE>   13
                              SELLING SHAREHOLDERS

         The Selling Shareholders are offering 637,001 shares of Common Stock
which may be acquired by them pursuant to awards under the Company's Long-Term
Incentive Stock Plan or the Company's prior Stock Option and Restricted Stock
Purchase Plan. The Grants are either currently exercisable or will vest on or
prior to October 31, 1999. There is no assurance that any of the Selling
Shareholders will offer for sale or sell any or all of the Common Stock offered
by them pursuant to this Prospectus.

         The following table sets forth certain information with respect to the
Selling Shareholders as of April 19, 1999, and includes awards which will vest
on or prior to October 31, 1999:

<TABLE>
<CAPTION>
---------------------------------------------------------------------------------------------------------------------------------

                                                                                                  NUMBER OF
                                               NUMBER OF        PERCENT OF       NUMBER OF       SHARES TO BE
                                             SHARES OWNED      CLASS OWNED     SHARES OFFERED    OWNED AFTER       PERCENT OF
NAME                                       PRIOR TO OFFERING     PRIOR TO          HEREBY       COMPLETION OF     CLASS OWNED
                                                                 OFFERING                        OFFERING(1)     AFTER OFFERING(1)
---------------------------------------------------------------------------------------------------------------------------------
<S>                                        <C>                 <C>             <C>              <C>              <C> 
Paul J. Kerz                                   1,079,317           6.1%           299,019          780,298            4.4%

Robert V. Nagelhout                              269,785           1.5%            64,916          204,869            1.2%

Alan L. Bendes                                    21,000            *              21,000             0                *

Donald J. Staffa                                 200,872           1.1%           148,155           52,717             *

Thomas J. Kazamek                                210,762           1.2%            78,713          132,049             *

Lewis D. Levetown                                 10,738            *               3,000            7,738             *  

Randolph G. Brown                                  3,250            *               2,500              750             *

William W. Neal                                   40,171            *               2,500           37,671             *

Galen D. Powers                                   17,685            *              12,198            5,487             *

Ellen A. Rudnick                                   7,000            *               2,500            4,500             *

Richard H. Stowe                                  64,114            *               2,500            61,61             *
---------------------------------------------------------------------------------------------------------------------------------
</TABLE>

----------
*        denotes percentage of ownership is less than 1%
(1)      Assumes all shares offered by this prospectus will be sold.


                                       4
<PAGE>   14
                              PLAN OF DISTRIBUTION

         The Selling Shareholders may, from time to time, offer all or part of
the shares acquired by them pursuant to awards on the over-the-counter market or
such national securities exchange upon which the Common Stock is traded at the
time of such sales, at prices prevailing at the time of such sales, or in
negotiated transactions. Selling Shareholders may also pledge their shares to
banks, brokers or other financial institutions as security for margin loans or
other financial accommodations that may be extended to such Selling
Shareholders, and any such pledgee institution may similarly offer, sell and
effect transactions in such shares. The Company will pay all expenses in
preparing and reproducing the Registration Statement of which this Prospectus is
a part, but will not receive any part of the proceeds of any sales of such
shares. In addition, any securities covered by this Prospectus which qualify for
sale pursuant to Rule 144 under the Act may be sold under Rule 144 rather than
pursuant to this Prospectus. The Selling Shareholders will pay the brokerage
commissions charged to sellers in connection with such sales. Each Selling
Shareholder (and pledgee) reserves the sole right to accept and, together with
its agents from time to time, to reject, in whole or in part, any proposed
purchase of shares to be made directly or through agents.

         The Company and the Selling Shareholders may enter into customary
agreements concerning indemnification and the provision of information in
connection with the sale of their shares of Common Stock.

                             VALIDITY OF THE SHARES

         The validity of the shares of Common Stock offered hereby will be
passed upon for the Company by Coleman, Rhine & Goodwin LLP, 750 Lexington
Avenue, New York, New York 10022. Partners of Coleman, Rhine & Goodwin LLP own
6,762 shares of Common Stock.

                                     EXPERTS

         The consolidated financial statements and financial statement schedule
of the Company as of October 31, 1998 and 1997, and for each of the years in the
three-year period ended October 31, 1998, have been incorporated by reference
herein and in the Registration Statement in reliance upon the report of KPMG
LLP, independent certified public accountants, incorporated by reference herein,
and upon the authority of said firm as experts in accounting and auditing.


                                       5
<PAGE>   15
                                  OTHER MATTERS

         The Business Corporation Law of the State of New York provides that,
under certain circumstances, directors, officers, employees or agents of a New
York corporation may be indemnified against expenses, payments, fines and
amounts actually and reasonably incurred by them in connection with settling, or
otherwise disposing of, suits or threatened suits, to which they are a party or
threatened to be named a party by reason of acting in any of such capacities, if
such person acted in good faith and in a manner such person reasonably believed
to be in, or not opposed to, the best interests of the corporation. The by-laws
of the Company provide for indemnification of officers and directors under the
circumstances, and to the extent, permitted by law. Insofar as indemnification
for liabilities arising under the Securities Act may be permitted to directors,
officers or persons controlling the Company pursuant to the foregoing provisions
and agreements, the Company has been informed that, in the opinion of the
Commission, such indemnification is against public policy as expressed in such
Securities Act and is therefore unenforceable.


                                       6
<PAGE>   16
                                   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 on Form S-8 to be signed on its behalf by the undersigned, thereto
duly authorized, in the City of New York, State of New York, on April 27, 1999.

                                      HEALTH MANAGEMENT SYSTEMS, INC.

                                      By: /s/ Paul J. Kerz
                                          -------------------------------------
                                          Paul J. Kerz
                                          President and Chief Executive Officer

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

<TABLE>
<S>                                           <C>                                             <C> 
/s/ Paul J. Kerz                              Chairman, President, Chief Executive Officer    April 27, 1999
----------------------------                  and Director
Paul J. Kerz


/s/ Robert V. Nagelhout                       Executive Vice President, Chief Operating       April 27, 1999
----------------------------                  Officer and Director
Robert V. Nagelhout

/s/ Alan L. Bendes                            Senior Vice President and Chief Financial and   April 27, 1999
----------------------------                  Accounting Officer
Alan L. Bendes

/s/ Donald J. Staffa                          Senior Vice President and Director              April 27, 1999
----------------------------
Donald J. Staffa


/s/ Randolph G. Brown                         Director                                        April 27, 1999
----------------------------
Randolph G. Brown

/s/ William W. Neal                           Director                                        April 27, 1999
----------------------------
William W. Neal

/s/ Galen D. Powers                           Director                                        April 27, 1999
----------------------------
Galen D. Powers

/s/ Ellen A. Rudnick                          Director                                        April 27, 1999
----------------------------
Ellen A. Rudnick

/s/ Richard H. Stowe                          Director                                        April 27, 1999
----------------------------
Richard H. Stowe

</TABLE>


                                      II-5
<PAGE>   17
                                  EXHIBIT INDEX

EXHIBIT
NUMBER                        DESCRIPTION

4                 Health Management Systems, Inc. 1999 Long-Term
                  Incentive Stock.

5                 Opinion of Coleman, Rhine & Goodwin LLP with
                  respect to the legality of the securities being
                  registered.

23.1              Consent of Coleman, Rhine & Goodwin LLP (included
                  in Exhibit 5).

23.2              Consent of KPMG LLP.

24                Powers of Attorney.
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1
     As filed with the Securities and Exchange Commission on April 27, 1999
                              Registration No. 333-

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                         HEALTH MANAGEMENT SYSTEMS, INC.
             (Exact name of Registrant as specified in its charter)

                                    New York
         (State or other jurisdiction of incorporation or organization)

                                   13-2770433
                     (I.R.S. Employer Identification Number)

                 401 Park Avenue South, New York, New York 10016
                    (Address of Principal Executive Offices)

                         HEALTH MANAGEMENT SYSTEMS, INC.
                       1999 LONG-TERM INCENTIVE STOCK PLAN
                            (Full title of the Plan)

                             Paul J. Kerz, President
                         Health Management Systems, Inc.
                              401 Park Avenue South
                            New York, New York 10016
                     (Name and address of agent for service)

                                  (212)685-4545
          (Telephone number, including area code, of agent for service)

                                   copies to:
                             Bruce S. Coleman, Esq.
                          Coleman, Rhine & Goodwin LLP
                              750 Lexington Avenue
                            New York, New York 10022
                                (212) 317-8880
2
                         CALCULATION OF REGISTRATION FEE
Proposed             Proposed
Title of                                            maximum              maximum
securities                     Amount               offering             aggregate            Amount of
to be                          to be                price per            offering             registration
registered                     registered           share (1)            price (1)            fee(2)
------------------------------ ------------------------ --------------- ----------------------- ---------------
Common Stock,                  4,751,356(2)             $4.53           $21,523,643                   $-
$.01 par value
------------------------------ ------------------------ --------------- ----------------------- ---------------
-------------------

(1)      Estimated pursuant to Rules 457(c) and 457(h) under the Securities Act
         of 1933, as amended, and based on the average of the high and low sale
         price reported on the Nasdaq-Amex National Market System of $4.53 on
         April 19, 1999.

(2)      Pursuant to Rule 429(a) under the Securities Act, this Registration
         Statement contains a combined prospectus that relates to Registration
         Statements Nos. 33-65560, 33-76638 and 33-3706 previously filed by the
         Registrant. Pursuant to Rule 429(b) under the Securities Act, all
         4,751,356 shares included herein are being carried forward from
         Registration Statements Nos. 33-65560, 33-76638 and 33-3706. Filing
         fees aggregating $32,198.87 were previously paid with such Registration
         Statements.

         Pursuant to Rule 416 under the Securities Act of 1933, there are also
being registered hereby such additional indeterminate number of shares of Common
Stock as may become issuable by reason of share splits, share dividends and
similar adjustments as set forth in the provisions of the Stock Option Plan and
the respective option agreements entered into thereunder.
3
                                EXPLANATORY NOTE

         This Registration Statement has been prepared in accordance with the
requirements of Form S-8 to register shares of Common Stock issuable pursuant to
the Registrant's 1999 Long-Term Incentive Stock Plan (the "Plan"). Under cover
of this Form S-8 is a Reoffer Prospectus prepared in accordance with the
requirements of Part I of Form S-3. The S-3 Reoffer Prospectus may be utilized
for reofferings of Common Stock acquired by certain Selling Shareholders through
participation in the Plan.
4
                                     PART I

              INFORMATION REQUIRED IN THE SECTION 10(A) PROSPECTUS

         Pursuant to Rule 428(b)(1) under the Securities Act of 1933, as amended
(the "Act"), an Information Statement with respect to the Health Management
Systems, Inc. 1999 Long-Term Incentive Stock Plan (the "Plan") will be
distributed to holders of stock options granted under such Plan. The Information
Statement, together with the documents incorporated by reference herein pursuant
to Item 3 of Part II below, taken together, constitute a Section 10(a)
prospectus and the Information Statement is hereby incorporated by reference in
this Registration Statement.

                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

ITEM 3.  INCORPORATION OF DOCUMENTS BY REFERENCE.

         There are hereby incorporated by reference herein the following
documents which have been filed with the Securities and Exchange Commission (the
"Commission"):

         (a) the Registrant's Annual Report on Form 10-K for its fiscal year
ended October 31, 1998, filed with the Commission on January 11, 1999;

         (b) the Registrant's Quarterly Report on Form 10-Q for the quarter
ended January 31, 1999, filed with the Commission on March 17, 1999;

         (c) all other reports filed pursuant to Section 13(a) or 15(d) of the
Securities Exchange Act of 1934, as amended (the "Exchange Act") since the end
of the Registrant's fiscal year ended October 31, 1998; and

         (d) the description of the Registrant's Common Stock contained in the
Registrant's Form 8-A filed with the Commission.

         All documents filed by the Registrant pursuant to Sections 13(a),
13(c), 14 and 15(d) of the Exchange Act after the date of this Registration
Statement and prior to the filing of a post-effective amendment hereto that
indicate that all securities offered have been sold or that deregisters all such
securities then remaining unsold, shall be deemed to be incorporated by
reference herein and to be a part hereof from the date of filing of such
documents.

                                      II-1
5
         Any statement contained in a document incorporated by reference herein
shall be deemed to be modified or superseded for purposes of this Registration
Statement to the extent that a statement contained herein or in any other
subsequently filed document that also is incorporated or 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.

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 722 of the New York Business Corporation Law (the "BCL")
provides that a corporation may indemnify directors and officers as well as
other employees and individuals against judgments, fines, amounts paid in
settlement and reasonable expenses, including attorneys' fees, in connection
with actions or proceedings, whether civil or criminal (other than an action by
or in the right of the corporation - a "derivative action"), if they acted in
good faith and in a manner they reasonably believed to be in or not opposed to
the best interests of the corporation, and, with respect to any criminal action
or proceeding, had no reasonable cause to believe their conduct was unlawful. A
similar standard is applicable in the case of derivative actions, except that
indemnification only extends to amounts paid in settlement and reasonable
expenses (including attorneys' fees) incurred in connection with the defense or
settlement of such actions, and the statute does not apply in respect of a
threatened action, or a pending action that is settled or otherwise disposed of,
and requires court approval before there can be any indemnification where the
person seeking indemnification has been found liable to the corporation. Section
721 of the BCL provides that Article 7 of the BCL is not exclusive of other
indemnification that may be granted by a corporation's certificate of
incorporation, disinterested director vote, stockholder vote, agreement or
otherwise. Article VIII, Section 7, of the Registrant's by-laws requires the
Registrant to indemnify its officers and directors to the fullest extent
permitted under the BCL.

                                      II-2
6
         Any amendment to or repeal of the Registrant's certificate of
incorporation or by-laws shall not adversely affect any right or protection of a
director of the Registrant for or with respect to any acts or omissions of such
director occurring prior to such amendment or repeal.

ITEM 7.  EXEMPTION FROM REGISTRATION CLAIMED.

         Not applicable.

ITEM 8.  EXHIBITS.

Exhibit
Number                     Description

4        Health Management Systems, Inc. 1999 Long-Term Incentive Stock Plan.

5        Opinion of Coleman, Rhine & Goodwin LLP with respect to the legality of
         the securities being registered.

23.1     Consent of Coleman, Rhine & Goodwin LLP (included in Exhibit 5).

23.2     Consent of KPMG LLP.

24       Powers of Attorney.

ITEM 9.  UNDERTAKINGS.

         The undersigned Registrant hereby undertakes:

         (a) to file, during any period in which offers or sales are being made,
a post-effective amendment to this Registration Statement to include any
material information with respect to the plan of distribution not previously
disclosed in the Registration Statement or any material change to such
information in the Registration Statement;

         (b) that, for the purpose of determining any liability under the 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; and

                                      II-3
7
         (c) 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.

         The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the Act, each filing of the Registrant's annual
report pursuant to Section 13(a) or 15(d) of the Exchange Act (and, where
applicable, each filing of an employee benefit plan's annual report pursuant to
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.

         Insofar as indemnification for liabilities arising under the Act may be
permitted to directors, officers and controlling persons of the Registrant
pursuant to the provisions described in Item 6 above, or otherwise, the
Registrant has been advised that in the opinion of the Commission such
indemnification is against public policy as expressed in the Act and is,
therefore, unenforceable. In the event that a claim for indemnification against
such liabilities (other than the payment by the Registrant of expenses incurred
or paid by a director, officer or controlling person of the Registrant 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, the Registrant 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 whether such indemnification by it is against public
policy as expressed in the Act and will be governed by the final adjudication of
such issue.

                                      II-4
8
REOFFER PROSPECTUS

                         HEALTH MANAGEMENT SYSTEMS, INC.
                              401 PARK AVENUE SOUTH
                            NEW YORK, NEW YORK 10016
                                  (212)685-4545

                                 637,001 Shares

                         Health Management Systems, Inc.

     Our Common Stock is listed on the Nasdaq-Amex National Market System under
the symbol "HMSY". The reported last sale price of the Common Stock on the
Nasdaq-Amex National Market System on April 19, 1999, was $4.44 per share.

     These shares of Common Stock may be issued to our officers, directors and
employees when they exercise stock options and other awards granted to them
under our Long-Term Incentive Stock Plan and our prior Stock Option and
Restricted Stock Purchase Plan. These shareholders may then sell these shares in
the open market or otherwise. We will not receive any part of the proceeds from
these sales.

         The shares have not been approved by the SEC or any state securities
commission, nor have these organizations determined that this prospectus is
accurate or complete. Any representation to the contrary is a criminal offense.

                  The date of this Prospectus is April 27, 1999
9
                                TABLE OF CONTENTS

Where You Can Find More Information.....................................1

About Health Management Systems, Inc. ("HMS")...........................2

Selling Shareholders....................................................4

Plan of Distribution....................................................5

Validity of the Shares..................................................5

Experts.................................................................5

Other Matters...........................................................6
10

                       WHERE YOU CAN FIND MORE INFORMATION

         We file annual, quarterly and special reports, proxy statements and
other information with the SEC. You may read and copy any document we file at
the SEC's public reference rooms in Washington, D.C., New York, New York and
Chicago, Illinois. Please call the SEC at 1-800-SEC-0330 for further information
on the public reference rooms. Our SEC filings are also available to the public
from our web site at www.hmsy.com or at the SEC's web site at www.sec.gov.

         The SEC allows us to "incorporate by reference" the information we file
with them, which means that we can disclose important information to you by
referring you to those documents. The information incorporated by reference is
considered to be part of this prospectus, and later information that we file
with the SEC will automatically update and supersede this information. We
incorporate by reference the documents listed below and any future filings made
with the SEC under Sections 13(a), 13(c), 14 or 15(d) of the Securities Exchange
Act of 1934 until the selling shareholders sell all the shares covered by this
prospectus. This prospectus is part of a registration statement we filed with
the SEC (Registration No. 333-____).

         We are incorporating the following documents by reference:

         Annual Report on Form 10-K for the year ended October 31, 1998; and

         Quarterly Report on Form 10-Q for the quarter ended January 31, 1999.

         You may request a copy of these filings, at no cost, by writing or
telephoning us at the following address:

                  Shareholder Services
                  Health Management Systems, Inc.
                  401 Park Avenue South
                  New York, New York 10016
                  (212)685-4545

         You should rely only on the information incorporated by reference or
provided in this prospectus or any supplement. We have not authorized anyone
else to provide you with different information. The selling shareholders will
not make an offer of these shares in any state where the offer is not permitted.
You should not assume that the information in this prospectus or any supplement

                                       1
11
is accurate as of any date other than the date on the front of those documents.

                                    ABOUT HMS

         HMS furnishes proprietary information management and data processing
products and services to healthcare providers and payors, including government
health service agencies. These services address the various types of data
generated by the interaction of the participants in the healthcare delivery
process: the providers of care, the third-party payors, and the patients.
Through its product and service offerings, the Company acts as an outsourcer of
information management functions addressing the operational, administrative,
financial, and clinical data that result from the rendering of healthcare
services to patients. The Company's product and service offerings benefit its
clients by enhancing revenue (achieved through improved reimbursability,
profitability, and/or collectability), accelerating cash flow, reducing
operating and administrative costs (by supplying advanced information
analytics), and improving decision-making capabilities (via the provision of
useful information).

         Healthcare providers receive payment for services from patients,
third-party payors, or a combination thereof. Third-party payors include
commercial insurance companies, governments or their fiscal agents and
intermediaries, health maintenance organizations, preferred provider
organizations, third-party administrators for self-insured companies, and
managed care companies. Although patients generally retain primary
responsibility for payment for all healthcare services, third-party payors bear
the preponderance of the responsibility for many charges for care. Obtaining
reimbursement from third-party payors has become increasingly difficult because
of frequent changes in reimbursement formulae and contractual requirements for
pre-admission certification and utilization review, and administrative
procedures instituted by third-party payors in an effort to control costs. To be
successful in obtaining payment from third-party payors, hospitals and other
healthcare providers require regulatory knowledge and technical skills to manage
complex data collection, integration, analysis, and accounts receivable
management functions. To ensure that program costs are not greater than
necessary, third-party payors require knowledge and skills analogous to those
required by providers.

                                       2
12
         Using the operational, financial, administrative, and clinical data
generated as part of the healthcare delivery process, the Company applies
proprietary software and other analytical tools to transform data into valuable
information that clients use to (i) minimize operating and administrative costs
while improving profitability, (ii) measure the quality of care, and (iii)
optimize the outcome of the transfer payment processes linking payors,
providers, and patients. Customers of the Company utilize the Company's products
and services to improve their decision-making and operating capabilities and to
achieve improved operational, administrative, financial, and clinical
performance. The Company believes its customers benefit from the Company's
unique understanding of the healthcare delivery and associated transfer payment
processes, from the perspective of both providers and payors.

                                       3
13
                              SELLING SHAREHOLDERS

         The Selling Shareholders are offering 637,001 shares of Common Stock
which may be acquired by them pursuant to awards under the Company's Long-Term
Incentive Stock Plan or the Company's prior Stock Option and Restricted Stock
Purchase Plan. The Grants are either currently exercisable or will vest on or
prior to October 31, 1999. There is no assurance that any of the Selling
Shareholders will offer for sale or sell any or all of the Common Stock offered
by them pursuant to this Prospectus.

         The following table sets forth certain information with respect to the
Selling Shareholders as of April 19, 1999, and includes awards which will vest
on or prior to October 31, 1999:
---------------------------------------------------------------------------------------------------------------------------------

                                                                                                  NUMBER OF
                                               NUMBER OF        PERCENT OF       NUMBER OF       SHARES TO BE
                                             SHARES OWNED      CLASS OWNED     SHARES OFFERED    OWNED AFTER       PERCENT OF
NAME                                       PRIOR TO OFFERING     PRIOR TO          HEREBY       COMPLETION OF     CLASS OWNED
                                                                 OFFERING                        OFFERING(1)     AFTER OFFERING(1)
---------------------------------------------------------------------------------------------------------------------------------
Paul J. Kerz                                   1,079,317           6.1%           299,019          780,298            4.4%

Robert V. Nagelhout                              269,785           1.5%            64,916          204,869            1.2%

Alan L. Bendes                                    21,000            *              21,000             0                *

Donald J. Staffa                                 200,872           1.1%           148,155           52,717             *

Thomas J. Kazamek                                210,762           1.2%            78,713          132,049             *

Lewis D. Levetown                                 10,738            *               3,000            7,738             *  

Randolph G. Brown                                  3,250            *               2,500              750             *

William W. Neal                                   40,171            *               2,500           37,671             *

Galen D. Powers                                   17,685            *              12,198            5,487             *

Ellen A. Rudnick                                   7,000            *               2,500            4,500             *

Richard H. Stowe                                  64,114            *               2,500            61,61             *
---------------------------------------------------------------------------------------------------------------------------------
----------
*        denotes percentage of ownership is less than 1%
(1)      Assumes all shares offered by this prospectus will be sold.

                                       4
14
                              PLAN OF DISTRIBUTION

         The Selling Shareholders may, from time to time, offer all or part of
the shares acquired by them pursuant to awards on the over-the-counter market or
such national securities exchange upon which the Common Stock is traded at the
time of such sales, at prices prevailing at the time of such sales, or in
negotiated transactions. Selling Shareholders may also pledge their shares to
banks, brokers or other financial institutions as security for margin loans or
other financial accommodations that may be extended to such Selling
Shareholders, and any such pledgee institution may similarly offer, sell and
effect transactions in such shares. The Company will pay all expenses in
preparing and reproducing the Registration Statement of which this Prospectus is
a part, but will not receive any part of the proceeds of any sales of such
shares. In addition, any securities covered by this Prospectus which qualify for
sale pursuant to Rule 144 under the Act may be sold under Rule 144 rather than
pursuant to this Prospectus. The Selling Shareholders will pay the brokerage
commissions charged to sellers in connection with such sales. Each Selling
Shareholder (and pledgee) reserves the sole right to accept and, together with
its agents from time to time, to reject, in whole or in part, any proposed
purchase of shares to be made directly or through agents.

         The Company and the Selling Shareholders may enter into customary
agreements concerning indemnification and the provision of information in
connection with the sale of their shares of Common Stock.

                             VALIDITY OF THE SHARES

         The validity of the shares of Common Stock offered hereby will be
passed upon for the Company by Coleman, Rhine & Goodwin LLP, 750 Lexington
Avenue, New York, New York 10022. Partners of Coleman, Rhine & Goodwin LLP own
6,762 shares of Common Stock.

                                     EXPERTS

         The consolidated financial statements and financial statement schedule
of the Company as of October 31, 1998 and 1997, and for each of the years in the
three-year period ended October 31, 1998, have been incorporated by reference
herein and in the Registration Statement in reliance upon the report of KPMG
LLP, independent certified public accountants, incorporated by reference herein,
and upon the authority of said firm as experts in accounting and auditing.

                                       5
15
                                  OTHER MATTERS

         The Business Corporation Law of the State of New York provides that,
under certain circumstances, directors, officers, employees or agents of a New
York corporation may be indemnified against expenses, payments, fines and
amounts actually and reasonably incurred by them in connection with settling, or
otherwise disposing of, suits or threatened suits, to which they are a party or
threatened to be named a party by reason of acting in any of such capacities, if
such person acted in good faith and in a manner such person reasonably believed
to be in, or not opposed to, the best interests of the corporation. The by-laws
of the Company provide for indemnification of officers and directors under the
circumstances, and to the extent, permitted by law. Insofar as indemnification
for liabilities arising under the Securities Act may be permitted to directors,
officers or persons controlling the Company pursuant to the foregoing provisions
and agreements, the Company has been informed that, in the opinion of the
Commission, such indemnification is against public policy as expressed in such
Securities Act and is therefore unenforceable.

                                       6
16
                                   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 on Form S-8 to be signed on its behalf by the undersigned, thereto
duly authorized, in the City of New York, State of New York, on April 27, 1999.

                                      HEALTH MANAGEMENT SYSTEMS, INC.

                                      By: /s/ Paul J. Kerz
                                          -------------------------------------
                                          Paul J. Kerz
                                          President and Chief Executive Officer

                  Pursuant to the requirements of the Securities Act of 1933,
this Registration Statement has been signed by the following persons in the
capacities indicated below on the respective dates set forth below.
/s/ Paul J. Kerz                              Chairman, President, Chief Executive Officer    April 27, 1999
----------------------------                  and Director
Paul J. Kerz

/s/ Robert V. Nagelhout                       Executive Vice President, Chief Operating       April 27, 1999
----------------------------                  Officer and Director
Robert V. Nagelhout

/s/ Alan L. Bendes                            Senior Vice President and Chief Financial and   April 27, 1999
----------------------------                  Accounting Officer
Alan L. Bendes

/s/ Donald J. Staffa                          Senior Vice President and Director              April 27, 1999
----------------------------
Donald J. Staffa

/s/ Randolph G. Brown                         Director                                        April 27, 1999
----------------------------
Randolph G. Brown

/s/ William W. Neal                           Director                                        April 27, 1999
----------------------------
William W. Neal

/s/ Galen D. Powers                           Director                                        April 27, 1999
----------------------------
Galen D. Powers

/s/ Ellen A. Rudnick                          Director                                        April 27, 1999
----------------------------
Ellen A. Rudnick

/s/ Richard H. Stowe                          Director                                        April 27, 1999
----------------------------
Richard H. Stowe
II-5
17
                                  EXHIBIT INDEX

EXHIBIT
NUMBER                        DESCRIPTION

4                 Health Management Systems, Inc. 1999 Long-Term
                  Incentive Stock.

5                 Opinion of Coleman, Rhine & Goodwin LLP with
                  respect to the legality of the securities being
                  registered.

23.1              Consent of Coleman, Rhine & Goodwin LLP (included
                  in Exhibit 5).

23.2              Consent of KPMG LLP.

24                Powers of Attorney.