<PAGE>   1
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION

                             WASHINGTON, D.C. 20549

                                    FORM 10-Q

                QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(D)
                     OF THE SECURITIES EXCHANGE ACT OF 1934

                FOR THE QUARTERLY PERIOD ENDED September 30, 1999

                        COMMISSION FILE NUMBER: 000-24539

                              ECLIPSYS CORPORATION
             (Exact name of registrant as specified in its charter)

DELAWARE                                          65-0632092
(State of Incorporation)                          (IRS Employer Identification
                                                  Number)

                            777 East Atlantic Avenue
                                    Suite 200
                              Delray Beach, Florida
                                      33483
                    (Address of principal executive offices)

                                 (561)-243-1440
                        (Telephone number of registrant)









            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 for the past
            90 days. Yes X No
                        ---  ---

            Indicate the number of shares outstanding of each of the issuer's
            classes of common stock as of the latest practicable date.

<TABLE>
<CAPTION>
                        Class                                         Shares outstanding as of October 31,1999
                        -----                                         ----------------------------------------

<S>                                                                                 <C>
            Common Stock, $.01 par value                                            34,947,979
            Non-voting Common Stock, $.01 par value                                    597,621
</TABLE>



<PAGE>   2

                              ECLIPSYS CORPORATION

                                    FORM 10-Q

                    FOR THE QUARTER ENDED SEPTEMBER 30, 1999

                                      INDEX

PART I.                 Financial Information

Item 1.                 Condensed Consolidated Balance Sheets (unaudited) - As
                        of September 30, 1999 and December 31, 1998

                        Condensed Consolidated Statements of Operations
                        (unaudited) - For the Three and Nine Months ended
                        September 30, 1999 and 1998

                        Condensed Consolidated Statements of Cash Flows
                        (unaudited) - For the Nine Months ended
                        September 30, 1999 and 1998

                        Notes to Condensed Consolidated Financial Statements
                        (unaudited) - For the Three and Nine Months ended
                        September 30, 1999 and 1998

Item 2.                 Management's Discussion and Analysis of Financial
                        Condition and Results of Operations


PART II.                Other Information

Item 6.                 Exhibits and Reports on Form 8-K


<PAGE>   3
PART I.
ITEM 1.

                              ECLISPSYS CORPORATION
                      CONDENSED CONSOLIDATED BALANCE SHEETS
                 AS OF SEPTEMBER 30, 1999 AND DECEMBER 31, 1998
                                 (IN THOUSANDS)
                                   (UNAUDITED)


<TABLE>
<CAPTION>
ASSETS                                         SEPTEMBER 30, 1999           DECEMBER 31, 1998
                                               ------------------           ------------------
<S>                                               <C>                          <C>
Current assets:
  Cash and cash equivalents                       $  36,545                    $  37,983
  Investments                                             -                       17,003
  Accounts receivable, net                           74,246                       62,324
  Inventory                                             426                          517
  Other current assets                               11,944                       10,013
                                                  ---------                    ---------
TOTAL CURRENT ASSETS                                123,161                      127,840

Fixed assets, net                                    13,342                       12,620
Capitalized software development costs, net           6,287                        5,248
Acquired technology, net                             39,809                       43,318
Intangible assets, net                               19,236                       25,928
Other assets                                          5,165                        6,060

                                                  ---------                    ---------
TOTAL ASSETS                                      $ 207,000                    $ 221,014
                                                  =========                    =========

LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities:
  Deferred revenue                                $  55,591                    $  51,366
  Current portion of long term debt                       -                        1,890
  Other current liabilities                          43,039                       48,860
                                                  ---------                    ---------
TOTAL CURRENT LIABILITIES                            98,630                      102,116

Deferred revenue                                      5,948                       16,700
Other long-term liabilities                           3,751                        3,756

STOCKHOLDERS' EQUITY
Preferred stock                                           -                            1
Common stock                                            355                          330
Common stock warrant                                    395                          395
Unearned stock compensation                            (353)                      (1,623)
Additional paid-in capital                          252,923                      241,975
Accumulated other comprehensive income                   64                           44
Accumulated deficit                                (154,713)                    (142,680)
                                                  ---------                    ---------
Total stockholders' equity                           98,671                       98,442


                                                  ---------                    ---------
TOTAL LIABILITIES AND STOCKHOLDERS' EQUITY        $ 207,000                    $ 221,014
                                                  =========                    =========
</TABLE>

         THE ACCOMPANYING NOTES ARE AN INTEGRAL PART OF THESE UNAUDITED
                   CONDENSED CONSOLIDATED FINANCIAL STATEMENTS




<PAGE>   4

                              ECLIPSYS CORPORATION
                 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
         FOR THE THREE AND NINE MONTHS ENDED SEPTEMBER 30, 1999 AND 1998
                (IN THOUSANDS EXCEPT SHARE AND PER SHARE AMOUNTS)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                              THREE MONTHS ENDED                         NINE MONTHS ENDED
                                                                 SEPTEMBER 30,                             SEPTEMBER 30,
                                                        --------------------------------      -------------------------------------
REVENUES                                                       1999              1998                     1999              1998
                                                               ----              ----                     ----              ----
<S>                                                          <C>               <C>                     <C>               <C>
  Systems and services                                       $ 58,361          $ 43,223                $ 168,097         $ 119,396
  Hardware                                                      6,469             3,708                   15,937             9,355
                                                        --------------------------------      -------------------------------------
TOTAL REVENUES                                                 64,830            46,931                  184,034           128,751
                                                        --------------------------------      -------------------------------------

COSTS AND EXPENSES
  Cost of systems and services revenues                        32,168            24,525                   93,375            69,746
  Cost of hardware revenues                                     5,408             3,130                   13,421             7,880
  Marketing and sales                                           9,587             7,080                   26,150            20,440
  Research and development                                     10,055             9,063                   34,149            25,800
  General and administrative                                    2,929             2,657                    9,033             7,690
  Depreciation and amortization                                 4,063             2,893                   11,734             8,750
  Write off of MSA                                                  -                 -                        -             7,193
  Stock compensation charge                                       982                 -                    1,987                 -
  Restructure charge                                            1,774                 -                    5,133                 -
  Pooling costs                                                     -                 -                    1,648                 -
                                                        --------------------------------      -------------------------------------
TOTAL COSTS AND EXPENSES                                       66,966            49,348                  196,630           147,499
                                                        --------------------------------      -------------------------------------

                                                        --------------------------------      -------------------------------------
LOSS FROM OPERATIONS                                           (2,136)           (2,417)                 (12,596)          (18,748)
                                                        --------------------------------      -------------------------------------

Interest income, net                                             (337)             (797)                    (945)           (1,835)


LOSS BEFORE INCOME TAXES                                       (1,799)           (1,620)                 (11,651)          (16,913)
PROVISION FOR INCOME TAXES                                          -             1,146                        -             4,252
                                                        --------------------------------      -------------------------------------

NET LOSS                                                       (1,799)           (2,766)                 (11,651)          (21,165)
                                                        --------------------------------      -------------------------------------

 DIVIDENDS AND ACCRETION ON MANDATORILY
 REDEEMABLE PREFERRED STOCK                                         -            (8,415)                       -           (10,928)

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

 NET LOSS AVAILABLE TO COMMON SHAREHOLDERS                   $ (1,799)        $ (11,181)               $ (11,651)        $ (32,093)
                                                        ================================      =====================================

 BASIC AND DILUTED NET LOSS PER COMMON SHARE                  $ (0.05)          $ (0.40)                 $ (0.34)          $ (1.52)
                                                        ================================      =====================================

 WEIGHTED AVERAGE COMMON SHARES OUTSTANDING                35,479,000        28,009,000               34,575,000        21,130,000
                                                        ================================      =====================================
</TABLE>






         THE ACCOMPANYING NOTES ARE AN INTEGRAL PART OF THESE UNAUDITED
                   CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

<PAGE>   5

                              ECLIPSYS CORPORATION
                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
              FOR THE NINE MONTHS ENDED SEPTEMBER 30, 1999 AND 1998
                                 (IN THOUSANDS)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                                            NINE MONTHS ENDED SEPTEMBER 30,
                                                                                           ---------------------------------
                                                                                                 1999              1998
                                                                                           ---------------    --------------
 OPERATING ACTIVITIES
<S>                                                                                            <C>             <C>
 Net Loss                                                                                      $(11,651)       $(21,165)
 Adjustments to reconcile net loss to net cash
 provided by operating activities:
             Depreciation and amortization                                                       31,747          21,692
             Provision for bad debts                                                              1,576           1,016
             Loss on sale of fixed assets                                                             -               8
             Tax benefit of stock option exercises                                                    -           1,145
             Write off of MSA                                                                         -           7,193
             Write off of capitalized software development costs                                  2,790               -
             Stock compensation expense                                                           2,250             132
             Changes in operating assets and liabilities, net of acquisitions:
               Accounts receivable                                                               (6,231)         (4,838)
               Inventory                                                                             91             327
               Other current assets                                                              (1,447)            984
               Other assets                                                                         289          (2,879)
               Deferred revenue                                                                  (8,406)         22,586
               Other current liabilities                                                         (6,340)         (1,101)
               Other liabilities                                                                     (5)            634
                                                                                               --------        --------
                        Total adjustments to reconcile net loss to net
                        cash provided by operating activities                                    16,314          46,899
                                                                                               --------        --------
                             NET CASH PROVIDED BY OPERATING ACTIVITIES                            4,663          25,734
                                                                                               ========        ========

 INVESTING ACTIVITIES
 Purchase of investments                                                                              -         (33,591)
 Maturities of investments                                                                       17,003           6,550
 Sales of investments                                                                                 -             250
 Purchase of fixed assets                                                                        (5,698)         (4,336)
 Capitalized software development costs                                                          (4,847)         (3,211)
 Acquisitions, net of cash acquired                                                             (20,000)              -
 Changes in other assets                                                                              -         (21,565)
                                                                                               --------        --------
                             NET CASH USED IN INVESTING ACTIVITIES                              (13,542)        (55,903)
                                                                                               ========        ========

 FINANCING ACTIVITIES
 Borrowings                                                                                      20,000          18,940
 Payments on borrowings                                                                         (20,000)        (35,088)
 Exercise of stock options                                                                        5,905             828
 Sale of common stock -initial public offering                                                        -          66,044
 Redemption of mandatorily redeemable preferred stock                                                 -         (38,771)
 Sale of preferred stock                                                                              -           9,000
 Employee stock purchase plan                                                                     1,893              59
 Distributions                                                                                     (377)           (305)
                                                                                               --------        --------
                             NET CASH PROVIDED BY FINANCING ACTIVITIES                            7,421          20,707
                                                                                               ========        ========

 EFFECT OF EXCHANGE RATE CHANGES ON CASH AND
      CASH EQUIVALENTS                                                                               20              33
                                                                                               --------        --------

 NET (DECREASE) IN CASH AND CASH EQUIVALENTS                                                     (1,438)         (9,429)

 CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD                                                  37,983          63,414
                                                                                               --------        --------
 CASH AND CASH EQUIVALENTS, END OF PERIOD                                                      $ 36,545        $ 53,985
                                                                                               ========        ========
</TABLE>






         THE ACCOMPANYING NOTES ARE AN INTEGRAL PART TO THESE UNAUDITED
                   CONDENSED CONSOLIDATED FINANCIAL STATEMENTS



<PAGE>   6

                              ECLIPSYS CORPORATION
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
         FOR THE THREE AND NINE MONTHS ENDED SEPTEMBER 30, 1999 AND 1998
                                   (UNAUDITED)

1.    BASIS OF PRESENTATION

      The condensed consolidated financial statements include all adjustments
      that, in the opinion of management, are necessary for a fair presentation
      of the results for the periods presented. All such adjustments are
      considered of a normal recurring nature. Quarterly results of operations
      are not necessarily indicative of annual results.

      Effective December 31, 1998, Eclipsys Corporation ("the Company")
      completed a merger with Transition Systems, Inc. ("Transition"). Effective
      February 17, 1999, the Company completed a merger with PowerCenter
      Systems, Inc. ("PCS"). Effective June 17, 1999, the Company completed a
      merger with MSI Solutions, Inc. and MSI Integrated Services, Inc.
      (collectively, "MSI"). Each of these mergers were accounted for as a
      pooling of interests and, accordingly, the condensed consolidated
      financial statements have been retroactively restated as if the mergers
      had occurred as of the beginning of the earliest period presented.

      The Company issued 1,104,000 and 2,375,000 of its common stock for all of
      the common stock outstanding of PCS and MSI, respectively. No adjustments
      were made to the net assets of either Company as a result of the
      acquisitions.

      Certain financial information and footnote disclosures normally included
      in financial statements prepared in accordance with generally accepted
      accounting principles have been condensed or omitted. These unaudited
      condensed consolidated financial statements should be read in conjunction
      with the consolidated financial statements and the notes thereto included
      in the Company's Annual Report on Form 10-K dated March 26, 1999.

      Certain prior year amounts have been reclassified to conform to the
      current year presentation in the accompanying condensed consolidated
      financial statements.



<PAGE>   7


                              ECLIPSYS CORPORATION
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
         FOR THE THREE AND NINE MONTHS ENDED SEPTEMBER 30, 1999 AND 1998
                                   (UNAUDITED)

2.    ACQUISITIONS

      The Transition, PCS and MSI acquisitions discussed in Note 1 were
      accounted for as poolings of interests, accordingly, all prior period
      amounts have been restated. A reconciliation between revenue and net loss
      as previously reported by the Company and as restated (unaudited) is as
      follows:

<TABLE>
<CAPTION>
                                         For the three               For the nine
                                         months ended                months ended
Revenue:                                 September 30, 1998          September 30, 1998
                                         ------------------          ------------------
<S>                                      <C>                         <C>
            As previously reported       $  36,160                   $  97,744
            Transition                       7,650                      22,595
            PCS                                319                         989
            MSI                              2,802                       7,423
                                         ---------                   ---------
            As restated                  $  46,931                   $ 128,751
Net Loss:
            As previously reported       $  (2,006)                  $ (16,828)
            Transition                        (635)                     (4,062)
            PCS                               (669)                     (1,624)
            MSI                                544                       1,349
                                         ---------                   ---------
            As restated                  $  (2,766)                  $ (21,165)
</TABLE>


      Effective March 31, 1999, the Company acquired the common stock of Intelus
      Corporation ("Intelus") and Med Data Systems, Inc. ("Med Data"), both
      wholly owned subsidiaries of Sungard Data Systems, Inc. for total
      consideration of $25.0 million in cash. The acquired entities both provide
      document imaging technology and workflow solutions to entities throughout
      the healthcare industry. The acquisition was accounted for as a purchase
      and, accordingly, the purchase price was allocated based on the fair value
      of the net assets acquired. As of March 31, 1999 the Company intended to
      dispose of Med Data.

      The purchase price is composed of and allocated of follows (in
      thousands):

<TABLE>
<CAPTION>
<S>                                            <C>
Cash                                            $ 25,000
Liabilities assumed                                4,306
                                                --------
                                                  29,306

Current assets                                     9,830
Fixed assets                                         778
                                                --------
                                                  10,608

Identifiable intangible assets
  (acquired technology)                         $ 18,698
                                                ========

</TABLE>

      Effective July 1, 1999, the Company sold Med Data for total a sales price
      of $5.0 million in cash. The Company reduced acquired technology
      originally recorded in the purchase by $4.4 million, which represented the
      difference between the sales price and the net assets sold.  No gain or
      loss was recorded.

      Unaudited pro forma results of operations as if the aforementioned
      acquisitions had occurred on January 1, 1998 is as follows (in thousands
      except per share data):

<TABLE>
<CAPTION>
                                             Nine months ended
                                               September 30,
                                         1999                  1998
                                       -------------------------------
<S>                                    <C>                 <C>
Revenues                               $ 187,525           $ 148,376
Net loss                               $ (12,090)          $ (29,181)
Basic and diluted loss per share       $    (.35)          $   (1.90)
</TABLE>






<PAGE>   8




                              ECLIPSYS CORPORATION
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
         FOR THE THREE AND NINE MONTHS ENDED SEPTEMBER 30, 1999 AND 1998
                                   (UNAUDITED)


3.    UNBILLED ACCOUNTS RECEIVABLE
      The current portion of unbilled accounts receivable were $17.9 million and
      $10.8 million as of September 30, 1999 and 1998, respectively, which is
      included in accounts receivable in the accompanying condensed consolidated
      balance sheet. The non-current portion of unbilled accounts receivable
      were $760,000 and  $2.1 million as of September 30, 1999 and 1998,
      respectively, which is included in other assets in the accompanying
      condensed consolidated balance sheet.

4.    POOLING COSTS
      Included in operating activities on the accompanying condensed
      consolidated statement of cash flows for the nine months ended September
      30, 1999 are $1.3 million of costs paid related to the poolings of
      Transition, PCS and MSI.

5.    RESTRUCTURING
      During the quarter ended September 30, 1999, the Company completed a
      restructure of its organization that began in the second quarter of 1999.
      In connection with the restructure, the Company incurred costs related to
      the closing of duplicate facilities and the termination of certain
      employees. Costs aggregating approximately $1.8 million and $3.4 million
      were incurred during the quarter ended September 30, 1999 and June 30,
      1999, respectively.

      As of September 30, 1999, accrued restructuring costs of $3.0 million are
      included in other current liabilities in the accompanying condensed
      consolidated balance sheet. Included in operating activities in the
      accompanying condensed consolidated statement of cash flows for the nine
      months ended September 30, 1999 are approximately $2.2 million of costs
      paid related to the restructuring.

6.    INVESTMENT IN HEALTHVISION
      During July 1999, the Company invested in Healthvision, Inc., a Dallas
      based, privately held internet healthcare company, in conjunction with
      VHA, Inc. and General Atlantic Partners, LLC. The Company purchased
      3,400,000 shares of common stock for $34,000, which represents 34% of the
      outstanding common stock on an if converted basis of Healthvision, Inc.
      The Company accounts for the investment using the equity method of
      accounting. This entity is a start-up enterprise that bears no
      relationship to the acquisition by Transition in December 1998.

7.    STOCK COMPENSATION CHARGE
      From time to time, the Company has granted options below fair market value
      and, accordingly, has recorded unearned stock compensation and recognizes
      stock compensation expense over the vesting period of the related stock
      options.

      During the second quarter 1999, in connection with the pooling of MSI,
      the Company recorded a stock compensation charge of $1.0 million
      related to the required accelerated vesting of certain stock options
      that were previously granted by MSI.

      During the quarter ended September 30, 1999, the Company recorded a stock
      compensation charge of $982,000 related to the accelerated vesting of
      certain employees' stock options in connection with their transfer to the
      newly formed Healthvision, Inc.

8.    CAPITALIZED SOFTWARE DEVELOPMENT COSTS
      During the second quarter 1999 and in connection with the pooling of MSI,
      the Company wrote off $2.8 million of capitalized software development
      costs related to duplicate products. The write off is included in research
      and development in the accompanying condensed consolidated financial
      statements.




<PAGE>   9



PART I.
ITEM 2.


         MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND
                              RESULTS OF OPERATIONS

      This report contains forward-looking statements. For this purpose, any
      statements contained herein that are not statements of historical fact may
      be deemed to be forward-looking statements. Without limiting the
      foregoing, the words "believes," "anticipates," "plans," "expects,"
      "intends," and similar expressions are intended to identify
      forward-looking statements. The important factors discussed under the
      caption "Certain Factors that May Affect Future Operating Results/Risk
      Factors," presented from time to time in the Company's filings with the
      Securities and Exchange Commission, among others, could cause actual
      results to differ materially from those indicated by forward-looking
      statements made herein. The Company undertakes no obligation to publicly
      update or revise any forward-looking statements, whether as a result of
      new information, future events or otherwise.

      OVERVIEW

      Eclipsys Corporation ("Eclipsys" or "the Company") is a healthcare
      information technology company delivering solutions that enable healthcare
      providers to achieve improved clinical, financial and administrative
      outcomes. The Company offers an integrated suite of core products in seven
      functional areas - clinical management, access management, patient
      financial management, health information management, strategic decision
      support, resource planning management and enterprise application
      integration. These products can be purchased in combination to provide an
      enterprise-wide solution or individually to address specific needs.
      Eclipsys' products have been designed specifically to deliver a measurable
      impact on outcomes, enabling Eclipsys' customers to quantify clinical
      benefits and return on investment in a precise and timely manner.
      Eclipsys' products can be integrated with a customer's existing
      information systems, which Eclipsys believes reduces overall cost of
      ownership and increases the attractiveness of its products. Eclipsys also
      provides outsourcing, remote processing and networking services to assist
      customers in meeting their healthcare information technology requirements.
      Eclipsys markets its products primarily to large hospitals, academic
      medical centers and integrated health networks. To provide direct and
      sustained customer contact, Eclipsys maintains decentralized sales,
      implementation and customer support teams in each of its eight North
      American regions.




<PAGE>   10



      The Company was formed in December 1995 and has grown primarily through a
      series of strategic acquisitions as follows:


<TABLE>
<CAPTION>
                                                                                           METHOD OF
                  TRANSACTION                                     DATE                    ACCOUNTING
                  -----------                                     ----                    ----------

<S>                                                               <C>                    <C>
      ALLTEL Healthcare Information Services, Inc.                1/24/97                 Purchase
      ("Alltel")

      SDK Medical Computer Services Corporation                   6/26/97                 Purchase
      ("SDK")

      Emtek Healthcare Systems                                    1/30/98                 Purchase
      ("Emtek") a division of Motorola, Inc.

      HealthVISION, Inc. (acquired by Transition)                 12/1/98                 Purchase
      ("HealthVISION")

      Transition Systems, Inc.                                    12/31/98                Pooling
      ("Transition")

      PowerCenter Systems, Inc.                                   2/17/99                 Pooling
      ("PCS")

      Intelus Corporation and Med Data Systems, Inc.              3/31/99                 Purchase
      ("Intelus" and "Med Data") wholly owned
      subsidiaries of Sungard Data Systems, Inc.

      MSI Solutions, Inc. and MSI Integrated                      6/17/99                 Pooling
      Services, Inc.
      (collectively, "MSI")
</TABLE>

      The condensed consolidated financial statements of the Company reflect the
      financial results of the purchased entities from the respective dates of
      the purchase. For all transactions accounted for using the pooling of
      interests method, the Company's condensed consolidated financial
      statements have been retroactively restated as if the transactions had
      occurred as of the beginning of the earliest period presented.

      RESULTS OF OPERATIONS

      SUMMARY
      Total revenues for the quarter ended September 30, 1999 increased 38% to
      $64.8 million compared with $46.9 million for the third quarter 1998. For
      the nine months ended September 30, 1999, total revenues increased 43% to
      $184.0 million compared to $128.8 million for the same period in 1998.

      Total costs and expenses for the quarter ended September 30, 1999
      increased 36% compared to the same period in 1998. For the nine months
      ended September 30, 1999 total costs and expenses increased 33% compared
      to the nine months ended September 30, 1998.


<PAGE>   11


      These changes in revenues and expenses combined to decrease net loss for
      the quarter ended September 30, 1999 by 35% to ($1.8) million compared to
      the same period in 1998. Included in the reported quarterly net losses
      were acquisition related amortization of intangible assets and certain
      non-recurring charges recorded in connection with the acquisitions of
      $11.1 million and $4.9 million for the quarter ended September 30, 1999
      and 1998, respectively.

      Year to date changes in revenues and expenses combined to decrease net
      loss for the nine months ended September 30, 1999 by 45% to ($11.7)
      million compared to the same period in 1998. Included in the reported nine
      month net losses were acquisition related amortization of intangible
      assets and certain non-recurring charges recorded in connection with the
      acquisitions of $36.2 million and $22.3 million for the nine months ended
      September 30, 1999 and 1998, respectively.

      REVENUES
      System and services revenues increased 35% to $58.4 million for the third
      quarter of 1999 compared to the same period in 1998 and 41% to $168.1
      million for the nine months ended September 30, 1999 compared to the same
      period in 1998. Contributing to this increase was the inclusion of the
      results of operations of HealthVISION and Intelus during the quarter and
      nine months of 1999, as well as new contracted business during 1998. The
      increase in new contracted business was a result of increased marketing
      efforts related to the regional re-alignment of the Company's operations
      completed in 1997 and the integration of the acquisitions.

      Hardware revenues increased 76% to $6.5 million for the third quarter of
      1999 compared to the same period in 1998 and 69% to $15.9 million for the
      nine months ended September 30, 1999 compared to the same period in 1998.
      The increase was primarily due to increased volume as a result of the
      acquisitions and new contracted business.

      EXPENSES
      Total cost of revenues increased 36% for the third quarter of 1999 and 38%
      for the year to date compared to the same periods in 1998. Increased costs
      of system, services and hardware associated with the growth in sales were
      partially offset by a reduction of certain expenses and realization of
      cost savings as a result of the integration of the acquisitions.

      Marketing and sales expenses increased 35% for the third quarter of 1999
      compared to the same period in 1998 and 28% for the nine months ended
      September 30, 1999 compared to the same period in 1998. The increase was
      primarily due to the addition of marketing and direct sales personnel
      following the acquisitions and the continued hiring of sales people.

      Total expenditures for research and development, including both
      capitalized and non-capitalized expenses increased 18% to $11.9 million
      for the third quarter 1999 compared to the same period in 1998 and 34% to
      $39.0 million for the nine months ended September 30, 1999 compared to the
      same period in 1998. The increase was due primarily to the acquisitions,
      the write-off of $2.8 million of capitalized software development costs
      related to duplicate products with no alternative future use due to the
      acquisition of MSI and the continued development of an enterprise-wide,
      web enabled, client server platform solution. Research and development
      expenses capitalized for the third quarter of 1999 increased $749,000
      compared to the same period in 1998 and $1,636,000 for the nine months
      ended September 30, 1999 compared to the same period in 1998. Increased
      capitalization was primarily the result of expenditures related to the
      development of an enterprise-wide, web enabled, client server platform
      solution.


<PAGE>   12



      General and administrative expenses increased 10% for the third quarter of
      1999 compared to the same period in 1998 and 17% for the nine months ended
      September 30, 1999 compared to the same period in 1998. The increase was
      primarily due to the addition of administrative and finance personnel
      following the acquisitions.

      Depreciation and amortization increased 40% for the third quarter of 1999
      compared to the same period in 1998 and 34% for the nine months ended
      September 30, 1999 compared to the same period in 1998. The increase for
      the quarter and year to date is primarily the result of an increase in
      goodwill amortization as a result of the HealthVISION acquisition.

      ACQUIRED IN-PROCESS RESEARCH AND DEVELOPMENT

      In connection with the Alltel, SDK and HealthVISION acquisitions, the
      Company wrote off acquired in-process research and development totaling
      $92.2 million and $7.0 million in 1997 and $2.4 million in 1998,
      respectively. These amounts were expensed as non-recurring charges on the
      respective acquisition dates. The Company continues to believe that the
      acquired in-process research and development will be successfully
      developed, but there can be no assurance that commercial viability of
      these products will be achieved.

      The value of the acquired in-process research and development was
      determined by estimating the projected net cash flows related to such
      products, including costs to complete the development of the technology
      and the future revenues to be earned upon commercialization of the
      products. These cash flows were discounted back to their net present
      value. The resulting projected net cash flows from such projects were
      based on management's estimates of revenues and operating profits related
      to such projects.

      Through September 30, 1999, revenues and operating profit attributable to
      the acquired in-process technology have not materially differed from the
      projections used in determining its value. Throughout 1999, the Company
      has continued the development of the in-process technology that was
      acquired in the transactions. To date, the Company is installing
      modules derived from the acquired in-process technology in various field
      trial sites that are expected to be activated by the end of 1999.
      Additionally, the Company has begun to successfully market certain aspects
      of the technology to new and existing customers. The Company expects to
      continue releasing products derived from the technology through 2001.
      Management continues to believe the projections used reasonably estimate
      the future benefits attributable to the in-process technology. However, no
      assurance can be given that deviations from these projections will not
      occur.

      If these projects to develop commercial products based on the acquired
      in-process technology are not successfully completed, the sales and
      profitability of the Company may be adversely affected in future periods.
      Additionally, the value of other intangible assets may become impaired.

      YEAR 2000 ISSUES

      Eclipsys has a Year 2000 Committee whose task is to evaluate the Company's
      Year 2000 readiness for both internal and external management information
      systems, recommend a plan of action to minimize disruption and execute the
      Company's Year 2000 plan. The Committee has developed a comprehensive Year
      2000 Plan. The Year 2000 Plan covers all significant internal and external
      management information systems.

      Eclipsys believes that all of its significant internal management
      information systems are currently Year 2000 compliant and, accordingly,
      does not anticipate any significant expenditures to remediate or replace
      existing internal-use systems.


<PAGE>   13

      All of the products currently offered by Eclipsys are Year 2000 compliant.
      Some of the products previously sold by Alltel, Emtek and Transition and
      installed in Eclipsys' customer base are not Year 2000 compliant. Eclipsys
      has developed and tested solutions for these non-compliant, installed
      products.

      In addition, because Eclipsys' products are often interfaced with a
      customer's existing third-party applications and certain Eclipsys'
      products include software licensed from third-party vendors, Eclipsys'
      products may experience difficulties interfacing with third-party,
      non-compliant applications. Based on currently available information,
      Eclipsys does not expect the cost of compliance related to interactions
      with non-compliant, third party systems to be material.

      Unexpected difficulties in implementing Year 2000 solutions for the
      installed Alltel, Emtek or Transition products or difficulties in
      interfacing with third-party products could adversely affect the
      Company. Additionally, apprehension in the marketplace over Year 2000
      compliance issues may lead businesses, including customers of the
      Company, to defer significant capital investments in information
      technology programs and software. They could elect to defer those
      investments either because they decide to focus their capital budgets on
      the expenditures necessary to bring their own existing systems into
      compliance or because they wish to purchase only software with a proven
      ability to process data after 1999.  If these deferrals are significant,
      the Company may not achieve expected revenue or earnings levels.

      BALANCE SHEET

      INVESTMENTS
      Investments decreased during the nine months ended September 30, 1999 due
      to the Company's reinvestment of maturities in highly liquid investments
      with original maturities of three months or less.

      ACCOUNTS RECEIVABLE
      Accounts receivables increased during the nine months ended September 30,
      1999 primarily due to the acquisitions of Intelus and activities related
      to the integration of Transition.

      ACQUIRED TECHNOLOGY
      Acquired technology decreased during the nine months ended September 30,
      1999 primarily due to amortization and a reduction in acquired
      technology related to the sale of Med Data.

      OTHER CURRENT LIABILITIES
      Other current liabilities decreased during the nine months ended September
      30, 1999 due to the timing of payments related to accounts payable and
      accrued expenses acquired from the acquisitions including deal costs of
      Transition and Intelus, and the payment of certain employee related
      expenses.

      LIQUIDITY AND CAPITAL RESOURCES

      During the nine months ended September 30, 1999, activities from
      operations provided the Company with $4.7 million in cash flow. Included
      in operations are approximately $1.3 million of costs paid directly
      related to the poolings of Transition, PCS and MSI during the nine months
      ended September 30, 1999. Additionally, included in operations is
      approximately $2.2 million of severance related to the Company's
      restructuring during the nine months ended September 30, 1999. The Company
      used $13.5 million for investing activities, which was primarily the
      result


<PAGE>   14

      of the acquisitions of Intelus and Med Data. Financing activities provided
      $7.4 million, primarily due to the exercise of stock options and the
      employee stock purchase plan.

      As of September 30, 1999, the Company had no amounts outstanding under its
      $50.0 million revolving credit facility.

      As of September 30, 1999, the Company had $36.5 million in cash and cash
      equivalents.

      Management believes that its available cash and cash equivalents,
      anticipated cash generated from its future operations and amounts
      available under the existing revolving credit facility will be sufficient
      to meet the Company's operating requirements for at least the next twelve
      months.



<PAGE>   15


            PART II.


            ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K
            (a)   Exhibits:  See Index to exhibits.
            (b)   Reports on Form 8-K: None


<PAGE>   16




                                   SIGNATURES

      Pursuant to the requirements 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.



                                                 ECLIPSYS CORPORATION



      Date:  November 15, 1999                   /s/ Robert J. Vanaria
                                                 ---------------------
                                                 Robert J. Vanaria
                                                 Chief Financial Officer




<PAGE>   17



                              ECLIPSYS CORPORATION
                                  EXHIBIT INDEX

<TABLE>
<CAPTION>
            EXHIBIT
               NO.                                     DESCRIPTION
               ---                                     -----------

             <S>         <C>
              2          Asset Purchase Agreement by and among Quadramed
                         Corporation, Eclipsys Corporation and Med Data
                         Systems, Inc dated July 1, 1999
              27         Financial Data Schedule (for SEC use only)
</TABLE>