<PAGE>   1
 
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
 
                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                           -------------------------
 
                                  FORM 10-K/A
                 ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d)
                     OF THE SECURITIES EXCHANGE ACT OF 1934
 
FOR THE FISCAL YEAR ENDED DECEMBER 31, 1998
 
COMMISSION FILE NUMBER 1-11831
 
                              SABRATEK CORPORATION
             (Exact name of registrant as specified in its charter)
 
<TABLE>
<S>                                              <C>
                  DELAWARE                                        36-3700639
       (State or other jurisdiction of                         (I.R.S. Employer
       incorporation or organization)                         Identification No.)
8111 NORTH ST. LOUIS AVENUE, SKOKIE, ILLINOIS                        60076
  (address of principal executive offices)                        (Zip Code)
</TABLE>
 
Registrant's telephone number, including area code: (847) 720-2400
 
Securities registered pursuant to Section 12(b) of the Act: None
 
Securities registered pursuant to Section 12(g) of the Act:
 
                                (TITLE OF CLASS)
                          Common Stock, $.01 Par Value
 
                                (TITLE OF CLASS)
                    Series B Preferred Stock Purchase Rights
 
     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes  X      No ___
 
     Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. [  ]
 
     The aggregate market value of the common stock, par value $.01 per share,
held by non-affiliates based upon the reported last sale price of the common
stock on March 17, 1999 was approximately $132,944,333.25.
 
     As of March 17, 1999, there were 9,875,584 shares of common stock, par
value $.01 per share, outstanding.
 
     The Index to Exhibits appears on page 47.
 
                      DOCUMENTS INCORPORATED BY REFERENCE
 
     The registrant's definitive 1999 Proxy Statement which will be filed
pursuant to Regulation 14A is incorporated by reference into Part III of this
Annual Report on Form 10-K.
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
<PAGE>   2
 
ITEM 6. SELECTED FINANCIAL DATA
 
     The selected financial data with respect to Sabratek's statements of
operations for each of the years in the five year period ended December 31, 1998
and the balance sheet data as of December 31, 1998, 1997, 1996, 1995 and 1994
are derived from Sabratek's audited financial statements. The financial data for
Sabratek should be read in conjunction with Sabratek's Financial Statements and
Notes thereto and "Management's Discussion and Analysis of Financial Condition
and Results of Operations," included elsewhere herein.
 
<TABLE>
<CAPTION>
                                                               YEAR ENDED DECEMBER 31,
                                                ------------------------------------------------------
                                                  1998       1997        1996        1995       1994
                                                  ----       ----        ----        ----       ----
                                                        (IN THOUSANDS, EXCEPT PER SHARE DATA)
<S>                                             <C>         <C>        <C>         <C>         <C>
STATEMENT OF OPERATIONS DATA:
Net sales...................................    $ 66,910    $43,058    $ 17,696    $  4,040    $ 3,315
Cost of sales...............................      29,966     18,720       8,748       2,902      2,481
Provision for inventory reserve.............       2,116         --          --          --         --
                                                --------    -------    --------    --------    -------
Gross margin................................      34,828     24,338       8,948       1,138        834
Selling, general and administrative
  expenses..................................      26,248     18,256       8,474       6,874      4,108
                                                --------    -------    --------    --------    -------
Operating income (loss).....................       8,580      6,082         474      (5,736)    (3,274)
Interest expense............................      (3,623)       (45)       (319)       (222)      (260)
Other income (expense), including interest
  income....................................       3,402      1,209         615         (78)       (21)
Stock appreciation rights(1)................          --         --      (1,628)         --         --
Provision for income taxes..................       3,487         --          --          --         --
                                                --------    -------    --------    --------    -------
Net income (loss)...........................    $  4,872    $ 7,246    $   (858)   $ (6,036)   $(3,555)
                                                ========    =======    ========    ========    =======
Basic income (loss) per share...............    $   0.47    $  0.75    $  (0.17)   $  (3.72)   $    --
                                                ========    =======    ========    ========    =======
Basic weighted average shares
  outstanding(2)............................      10,316      9,614       5,143       1,622         --
                                                ========    =======    ========    ========    =======
Diluted income (loss) per share.............    $   0.44    $  0.67    $  (0.17)   $  (3.72)   $    --
                                                ========    =======    ========    ========    =======
Diluted weighted average shares
  outstanding(2)............................      11,146     10,895       5,143       1,622         --
                                                ========    =======    ========    ========    =======
</TABLE>
 
<TABLE>
<CAPTION>
                                                               YEAR ENDED DECEMBER 31,
                                                ------------------------------------------------------
                                                  1998       1997        1996        1995       1994
                                                  ----       ----        ----        ----       ----
                                                                    (IN THOUSANDS)
<S>                                             <C>         <C>        <C>         <C>         <C>
BALANCE SHEET DATA:
Working capital.............................    $ 70,969    $48,156    $ 24,587    $ (1,101)   $   999
Total assets................................     152,679     71,167      32,951       4,179      3,338
Short-term debt (including current portion
  of long term obligations)(3)..............          33         25         303         775         91
Debt and Long-term obligations..............      85,216        264          24       2,512        464
Accumulated deficit.........................      (2,192)    (7,064)    (14,310)    (13,452)    (7,416)
Total stockholders' equity (deficit)........      58,029     64,415      28,650      (2,821)     1,151
</TABLE>
 
-------------------------
(1) For the year ended December 31, 1996, a non-recurring charge in the amount
    of approximately $1.6 million was recorded to recognize obligations under
    certain stock appreciation rights in connection with Sabratek's June 1996
    initial public offering.
 
(2) See Note (2) to the Financial Statements for an explanation of the
    calculation of weighted average shares outstanding.
 
(3) Includes capital lease obligations.
 
                                       19
<PAGE>   3
 
                                   SIGNATURES
 
     Pursuant to the Requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the registrant has duly caused this report to be signed on
its behalf by the undersigned, thereunto duly authorized.
 
                                          SABRATEK CORPORATION
 
                                          By:       /s/ K. SHAN PADDA
 
                                            ------------------------------------
                                            Chairman and Chief Executive Officer
 
                                                      April 9, 1999
 
                                          --------------------------------------
                                                          (Date)
 
     Pursuant to the requirements of the Securities Exchange Act of 1934, this
report has been signed below by the following persons on behalf of the
registrant and in the capacities indicated on April 9, 1999.
 
<TABLE>
<CAPTION>
                  SIGNATURE                                          TITLE
                  ---------                                          -----
<C>                                              <S>
              /s/ K. SHAN PADDA                  Chairman of the Board, Chief Executive
---------------------------------------------    Officer and Director
                K. Shan Padda
 
            /s/ DORON C. LEVITAS                 Vice Chairman of the Board, Chief
---------------------------------------------    Administrative Officer, Vice
              Doron C. Levitas                   President -- International Operations,
                                                 Secretary and Director
 
            /s/ STEPHEN L. HOLDEN                President and Treasurer
---------------------------------------------
              Stephen L. Holden
 
            /s/ PAUL S. JUREWICZ                 Senior Vice President and Chief Financial
---------------------------------------------    Officer
              Paul S. Jurewicz
 
             /s/ SCOTT SKOOGLUND                 Vice President -- Finance and Assistant
---------------------------------------------    Secretary, Principal Accounting Officer
               Scott Skooglund
 
           /s/ WILLIAM D. LAUTMAN                Director
---------------------------------------------
             William D. Lautman
 
             /s/ L. PETER SMITH                  Director
---------------------------------------------
               L. Peter Smith
 
          /s/ FRANCIS V. COOK, M.D.              Director
---------------------------------------------
            Francis V. Cook, M.D.
 
          /s/ EDSON W. SPENCER, JR.              Director
---------------------------------------------
            Edson W. Spencer, Jr.
 
              /s/ MARVIN SAMSON                  Director
---------------------------------------------
                Marvin Samson
</TABLE>
 
                                       48
<PAGE>   4
 
<TABLE>
<CAPTION>
                  SIGNATURE                                          TITLE
                  ---------                                          -----
<C>                                              <S>
           /s/ WILLIAM H. LOMICKA                Director
---------------------------------------------
             William H. Lomicka
 
              /s/ MARK LAMPERT                   Director
---------------------------------------------
                Mark Lampert
</TABLE>
 
                                       49