<PAGE>   1
As filed with the Securities and Exchange Commission on May 7, 1999
                                                        Registration No. 333-___
================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM S-8

                          REGISTRATION STATEMENT UNDER
                           THE SECURITIES ACT OF 1933

                              MKS INSTRUMENTS, INC.
             (Exact Name of Registrant as Specified in Its Charter)

                                  MASSACHUSETTS
         (State or Other Jurisdiction of Incorporation or Organization)

                                   04-2277512
                      (I.R.S. Employer Identification No.)

SIX SHATTUCK ROAD, ANDOVER, MASSACHUSETTS                            01810
 (Address of Principal Executive Offices)                          (Zip Code)

                 AMENDED AND RESTATED 1995 STOCK INCENTIVE PLAN
                            (Full Title of the Plan)

                              MARK G. BORDEN, ESQ.
                                HALE AND DORR LLP
                                 60 STATE STREET
                           BOSTON, MASSACHUSETTS 02109
                     (Name and Address of Agent for Service)

                                 (617) 526-6000
          (Telephone Number, Including Area Code, of Agent For Service)


================================================================================

                         CALCULATION OF REGISTRATION FEE

================================================================================
<TABLE>
<CAPTION>
                                             PROPOSED                                                
  TITLE OF                                    MAXIMUM         PROPOSED MAXIMUM        AMOUNT OF
 SECURITIES               AMOUNT             OFFERING        AGGREGATE OFFERING     REGISTRATION
    TO BE                  TO BE             PRICE PER              PRICE                FEE
 REGISTERED             REGISTERED             SHARE                                              
----------------------------------------------------------------------------------------------------
<S>                     <C>                   <C>             <C>                      <C>     
Common Stock,                                                                                        
no par value            3,750,000             $12.63(1)       $  47,362,500(1)         $ 13,167
====================================================================================================
</TABLE>

(1)      Estimated solely for the purpose of calculating the registration fee,
         and based upon the average of the high and low sale prices of the
         Common Stock on the Nasdaq National Market on May 5, 1999 in accordance
         with Rules 457(c) and 457(h) of the Securities Act of 1933, as amended.
================================================================================


<PAGE>   2


PART I.  INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS

         The information required by Part I is included in documents sent or
given to participants in the Registrant's Amended and Restated 1995 Stock
Incentive Plan pursuant to Rule 428(b)(1) of the Securities Act of 1933, as
amended (the "Securities Act").


PART II. INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.  INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE

         The Registrant is subject to the informational and reporting
requirements of Sections 13(a), 14 and 15(d) of the Securities Exchange Act of
1934, as amended (the "Exchange Act"), and in accordance therewith files
reports, proxy statements and other information with the Securities and Exchange
Commission (the "Commission"). The following documents, which are filed with the
Commission, are incorporated in this Registration Statement by reference:

                  (1) The Registrant's latest prospectus filed pursuant to Rule
         424(b) under the Securities Act that contains audited financial
         statements for the Registrant's latest fiscal year for which such
         statements have been filed.

                  (2) All other reports filed pursuant to Section 13(a) or 15(d)
         of the Exchange Act since the end of the fiscal year covered by the
         prospectus referred to in (1) above.

                  (3) The description of the common stock of the Registrant, no
         par value per share (the "Common Stock"), contained in the Registration
         Statement on Form 8-A filed by the Registrant with the Commission on
         March 2, 1999.

         All documents subsequently filed by the Registrant pursuant to Sections
13(a), 13(c), 14 and 15(d) of the Exchange Act, prior to the filing of a
post-effective amendment which indicates that all shares of Common Stock offered
hereby have been sold or which deregisters all shares of Common Stock then
remaining unsold, shall be deemed to be incorporated by reference herein and to
be part hereof from the date of the filing of such documents.

Item 4.  DESCRIPTION OF SECURITIES                      

         Not applicable.

Item 5.  INTERESTS OF NAMED EXPERTS AND COUNSEL

         Not applicable.



                                      II-1
<PAGE>   3


Item 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS

         Section 67 of Chapter 156B of the Massachusetts General Laws ("Section
67") provides that a corporation may indemnify its directors and officers to the
extent specified in or authorized by (i) the articles of organization, (ii) a
by-law adopted by the stockholders or (iii) a vote adopted by the holders of a
majority of the shares of stock entitled to vote on the election of directors.
In all instances, the extent to which a corporation provides indemnification to
its directors and officers under Section 67 is optional. In its Restated
Articles of Organization (the "Articles of Organization"), the Registrant has
elected to commit to provide indemnification to its directors and officers in
specified circumstances. Generally, Article 6 of the Registrant's Articles of
Organization provides that the Registrant shall indemnify directors and officers
of the Registrant against liabilities and expenses arising out of legal
proceedings brought against them by reason of their status or service as
directors or officers or by reason of their agreeing to serve, at the request of
the Registrant, as a director or officer with another organization. Under this
provision, a director or officer of the Registrant shall be indemnified by the
Registrant for all costs and expenses (including attorneys' fees), judgments,
liabilities and amounts paid in settlement of such proceedings, even if he is
not successful on the merits, if he acted in good faith in the reasonable belief
that his action was in the best interests of the Registrant. The Board of
Directors may authorize advancing litigation expenses to a director or officer
at his request upon receipt of an undertaking by any such director or officer to
repay such expenses if it is ultimately determined that he is not entitled to
indemnification for such expenses.

         Article 6 of the Registrant's Articles of Organization eliminates the
personal liability of the Registrant's directors to the Registrant or its
stockholders for monetary damages for breach of a director's fiduciary duty,
except to the extent Chapter 156B of the Massachusetts General Laws prohibits
the elimination or limitation of such liability.

         The Registrant has obtained directors and officers liability insurance
for the benefit of its directors and certain officers.

Item 7.  EXEMPTION FROM REGISTRATION CLAIMED

         Not applicable.

Item 8.  EXHIBITS

         The Exhibit Index immediately preceding the exhibits is incorporated
herein by reference.

Item 9.  UNDERTAKINGS





                                      II-2
<PAGE>   4

         1.       The Registrant hereby undertakes:

                  (1) 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;

                  (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.

         2. The Registrant hereby undertakes that, for purposes of determining
any liability under the Securities Act, each filing of the Registrant's annual
report pursuant to Section 13(a) or Section 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 the 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 in the initial bona fide offering thereof.

         3. Insofar as indemnification for liabilities arising under the
Securities Act may be permitted to directors, officers and controlling persons
of the Registrant pursuant to the foregoing provisions, or otherwise, the
Registrant 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 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 Securities Act and will be governed by the final
adjudication of such issue.





                                      II-3
<PAGE>   5

                                   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 Andover, Commonwealth of Massachusetts, on this 7th
day of May, 1999.


                                                   MKS INSTRUMENTS, INC.



                                               By: /s/ John R. Bertucci
                                                   -----------------------------

                                                   John R. Bertucci
                                                   Chairman of the Board,
                                                   President and Chief Executive
                                                   Officer





                                      II-4
<PAGE>   6





                                POWER OF ATTORNEY

         We, the undersigned officers and directors of MKS Instruments, Inc.,
hereby severally constitute John R. Bertucci, Ronald C. Weigner and Mark G.
Borden, and each of them singly, our true and lawful attorneys with full power
to them, and each of them singly, to sign for us and in our names in the
capacities indicated below, the Registration Statement on Form S-8 filed
herewith and any and all subsequent amendments to said Registration Statement,
and generally to do all such things in our names and behalf in our capacities as
officers and directors to enable MKS Instruments, Inc. to comply with all
requirements of the Securities and Exchange Commission, hereby ratifying and
confirming our signatures as they may be signed by said attorneys, or any of
them, to said Registration Statement and any and all amendments thereto.

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



       Signature                         Title                         Date
       ---------                         -----                         ----

/s/ John R. Bertucci            Chairman of the Board, President     May 7, 1999
----------------------          and Chief Executive Officer     
John R. Bertucci                (Principal Executive Officer)   


/s/ Ronald C. Weigner           Vice President and Chief             May 7, 1999
----------------------          Financial Officer               
Ronald C. Weigner                                               

/s/ Richard S. Chute             Director                            May 7, 1999
----------------------
Richard S. Chute

/s/ Owen W. Robbins              Director                            May 7, 1999
----------------------
Owen W. Robbins

/s/ Robert J. Therrien           Director                            May 7, 1999
----------------------
Robert J. Therrien

/s/ Louis P. Valente             Director                            May 7, 1999
----------------------
Louis P. Valente









                                      II-5
<PAGE>   7


                                  EXHIBIT INDEX



        Exhibit
        Number                          Description
        ------                          -----------


         4(1)     Specimen Certificate for shares of Common Stock, no par value
                  per share, of the Registrant

         5        Opinion of Hale and Dorr LLP

         23.1     Consent of Hale and Dorr LLP (included in Exhibit 5)

         23.2     Consent of PricewaterhouseCoopers LLP

         24       Power of Attorney (included on the signature page of this
                  Registration Statement)
















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

      1     Incorporated herein by reference to the Registrant's Registration
            Statement on Form S-1 (Commission File No. 333-71363).


                                      II-6
[{"type": "S-8", "sequence": "1", "description": "AMENDED AND RESTATED 1995 STOCK INCENTIVE PLAN", "secsgml_size_bytes": 15028}]
{"company-data": {"conformed-name": "MKS INSTRUMENTS INC", "cik": "0001049502", "assigned-sic": "3823", "irs-number": "042277512", "state-of-incorporation": "MA", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-78071", "film-number": "99614375"}, "business-address": {"street1": "512 SHATTUCK RD", "city": "ANDOVER", "state": "MA", "zip": "01810", "phone": "9789752350"}, "mail-address": {"street1": "512 SHATTUCK ROAD", "city": "ANDOVER", "state": "MA", "zip": "01810"}}
1
As filed with the Securities and Exchange Commission on May 7, 1999
                                                        Registration No. 333-___
================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM S-8

                          REGISTRATION STATEMENT UNDER
                           THE SECURITIES ACT OF 1933

                              MKS INSTRUMENTS, INC.
             (Exact Name of Registrant as Specified in Its Charter)

                                  MASSACHUSETTS
         (State or Other Jurisdiction of Incorporation or Organization)

                                   04-2277512
                      (I.R.S. Employer Identification No.)

SIX SHATTUCK ROAD, ANDOVER, MASSACHUSETTS                            01810
 (Address of Principal Executive Offices)                          (Zip Code)

                 AMENDED AND RESTATED 1995 STOCK INCENTIVE PLAN
                            (Full Title of the Plan)

                              MARK G. BORDEN, ESQ.
                                HALE AND DORR LLP
                                 60 STATE STREET
                           BOSTON, MASSACHUSETTS 02109
                     (Name and Address of Agent for Service)

                                 (617) 526-6000
          (Telephone Number, Including Area Code, of Agent For Service)

================================================================================

                         CALCULATION OF REGISTRATION FEE

================================================================================
PROPOSED                                                
  TITLE OF                                    MAXIMUM         PROPOSED MAXIMUM        AMOUNT OF
 SECURITIES               AMOUNT             OFFERING        AGGREGATE OFFERING     REGISTRATION
    TO BE                  TO BE             PRICE PER              PRICE                FEE
 REGISTERED             REGISTERED             SHARE                                              
----------------------------------------------------------------------------------------------------
Common Stock,                                                                                        
no par value            3,750,000             $12.63(1)       $  47,362,500(1)         $ 13,167
====================================================================================================
(1)      Estimated solely for the purpose of calculating the registration fee,
         and based upon the average of the high and low sale prices of the
         Common Stock on the Nasdaq National Market on May 5, 1999 in accordance
         with Rules 457(c) and 457(h) of the Securities Act of 1933, as amended.
================================================================================
2

PART I.  INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS

         The information required by Part I is included in documents sent or
given to participants in the Registrant's Amended and Restated 1995 Stock
Incentive Plan pursuant to Rule 428(b)(1) of the Securities Act of 1933, as
amended (the "Securities Act").

PART II. INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.  INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE

         The Registrant is subject to the informational and reporting
requirements of Sections 13(a), 14 and 15(d) of the Securities Exchange Act of
1934, as amended (the "Exchange Act"), and in accordance therewith files
reports, proxy statements and other information with the Securities and Exchange
Commission (the "Commission"). The following documents, which are filed with the
Commission, are incorporated in this Registration Statement by reference:

                  (1) The Registrant's latest prospectus filed pursuant to Rule
         424(b) under the Securities Act that contains audited financial
         statements for the Registrant's latest fiscal year for which such
         statements have been filed.

                  (2) All other reports filed pursuant to Section 13(a) or 15(d)
         of the Exchange Act since the end of the fiscal year covered by the
         prospectus referred to in (1) above.

                  (3) The description of the common stock of the Registrant, no
         par value per share (the "Common Stock"), contained in the Registration
         Statement on Form 8-A filed by the Registrant with the Commission on
         March 2, 1999.

         All documents subsequently filed by the Registrant pursuant to Sections
13(a), 13(c), 14 and 15(d) of the Exchange Act, prior to the filing of a
post-effective amendment which indicates that all shares of Common Stock offered
hereby have been sold or which deregisters all shares of Common Stock then
remaining unsold, shall be deemed to be incorporated by reference herein and to
be part hereof from the date of the filing of such documents.

Item 4.  DESCRIPTION OF SECURITIES                      

         Not applicable.

Item 5.  INTERESTS OF NAMED EXPERTS AND COUNSEL

         Not applicable.

                                      II-1
3

Item 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS

         Section 67 of Chapter 156B of the Massachusetts General Laws ("Section
67") provides that a corporation may indemnify its directors and officers to the
extent specified in or authorized by (i) the articles of organization, (ii) a
by-law adopted by the stockholders or (iii) a vote adopted by the holders of a
majority of the shares of stock entitled to vote on the election of directors.
In all instances, the extent to which a corporation provides indemnification to
its directors and officers under Section 67 is optional. In its Restated
Articles of Organization (the "Articles of Organization"), the Registrant has
elected to commit to provide indemnification to its directors and officers in
specified circumstances. Generally, Article 6 of the Registrant's Articles of
Organization provides that the Registrant shall indemnify directors and officers
of the Registrant against liabilities and expenses arising out of legal
proceedings brought against them by reason of their status or service as
directors or officers or by reason of their agreeing to serve, at the request of
the Registrant, as a director or officer with another organization. Under this
provision, a director or officer of the Registrant shall be indemnified by the
Registrant for all costs and expenses (including attorneys' fees), judgments,
liabilities and amounts paid in settlement of such proceedings, even if he is
not successful on the merits, if he acted in good faith in the reasonable belief
that his action was in the best interests of the Registrant. The Board of
Directors may authorize advancing litigation expenses to a director or officer
at his request upon receipt of an undertaking by any such director or officer to
repay such expenses if it is ultimately determined that he is not entitled to
indemnification for such expenses.

         Article 6 of the Registrant's Articles of Organization eliminates the
personal liability of the Registrant's directors to the Registrant or its
stockholders for monetary damages for breach of a director's fiduciary duty,
except to the extent Chapter 156B of the Massachusetts General Laws prohibits
the elimination or limitation of such liability.

         The Registrant has obtained directors and officers liability insurance
for the benefit of its directors and certain officers.

Item 7.  EXEMPTION FROM REGISTRATION CLAIMED

         Not applicable.

Item 8.  EXHIBITS

         The Exhibit Index immediately preceding the exhibits is incorporated
herein by reference.

Item 9.  UNDERTAKINGS

                                      II-2
4

         1.       The Registrant hereby undertakes:

                  (1) 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;

                  (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.

         2. The Registrant hereby undertakes that, for purposes of determining
any liability under the Securities Act, each filing of the Registrant's annual
report pursuant to Section 13(a) or Section 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 the 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 in the initial bona fide offering thereof.

         3. Insofar as indemnification for liabilities arising under the
Securities Act may be permitted to directors, officers and controlling persons
of the Registrant pursuant to the foregoing provisions, or otherwise, the
Registrant 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 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 Securities Act and will be governed by the final
adjudication of such issue.

                                      II-3
5

                                   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 Andover, Commonwealth of Massachusetts, on this 7th
day of May, 1999.

                                                   MKS INSTRUMENTS, INC.

                                               By: /s/ John R. Bertucci
                                                   -----------------------------

                                                   John R. Bertucci
                                                   Chairman of the Board,
                                                   President and Chief Executive
                                                   Officer

                                      II-4
6

                                POWER OF ATTORNEY

         We, the undersigned officers and directors of MKS Instruments, Inc.,
hereby severally constitute John R. Bertucci, Ronald C. Weigner and Mark G.
Borden, and each of them singly, our true and lawful attorneys with full power
to them, and each of them singly, to sign for us and in our names in the
capacities indicated below, the Registration Statement on Form S-8 filed
herewith and any and all subsequent amendments to said Registration Statement,
and generally to do all such things in our names and behalf in our capacities as
officers and directors to enable MKS Instruments, Inc. to comply with all
requirements of the Securities and Exchange Commission, hereby ratifying and
confirming our signatures as they may be signed by said attorneys, or any of
them, to said Registration Statement and any and all amendments thereto.

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

       Signature                         Title                         Date
       ---------                         -----                         ----

/s/ John R. Bertucci            Chairman of the Board, President     May 7, 1999
----------------------          and Chief Executive Officer     
John R. Bertucci                (Principal Executive Officer)   

/s/ Ronald C. Weigner           Vice President and Chief             May 7, 1999
----------------------          Financial Officer               
Ronald C. Weigner                                               

/s/ Richard S. Chute             Director                            May 7, 1999
----------------------
Richard S. Chute

/s/ Owen W. Robbins              Director                            May 7, 1999
----------------------
Owen W. Robbins

/s/ Robert J. Therrien           Director                            May 7, 1999
----------------------
Robert J. Therrien

/s/ Louis P. Valente             Director                            May 7, 1999
----------------------
Louis P. Valente

                                      II-5
7

                                  EXHIBIT INDEX

        Exhibit
        Number                          Description
        ------                          -----------

         4(1)     Specimen Certificate for shares of Common Stock, no par value
                  per share, of the Registrant

         5        Opinion of Hale and Dorr LLP

         23.1     Consent of Hale and Dorr LLP (included in Exhibit 5)

         23.2     Consent of PricewaterhouseCoopers LLP

         24       Power of Attorney (included on the signature page of this
                  Registration Statement)

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

      1     Incorporated herein by reference to the Registrant's Registration
            Statement on Form S-1 (Commission File No. 333-71363).

                                      II-6