<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, 1998

                        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, 1998
      -----                                       -----------------------------------------

<S>                                                                <C>       
Common Stock, $.01 par value                                       19,443,986
Non-voting Common Stock, $.01 par value                               896,431
</TABLE>


<PAGE>   2

                              ECLIPSYS CORPORATION

                                    FORM 10-Q

                    FOR THE QUARTER ENDED SEPTEMBER 30, 1998

                                      INDEX

<TABLE>
<CAPTION>
PART I.         Financial Information

<S>       <C>                                                               
Item 1.   Condensed Consolidated Balance Sheets - September 30, 1998 (unaudited) and 
                December 31, 1997

          Condensed Consolidated Statements of Operations - For the Three and Nine Months 
                ended September 30, 1998 and 1997 (unaudited)

          Condensed Consolidated Statements of Cash Flows - For the Nine Months ended 
                September 30, 1998 and 1997 (unaudited)

          Notes to Condensed Consolidated Financial Statements

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


PART II.        Other Information

Item 2.   Changes in Securities

Item 4.   Submission of Matters to a Vote of Security Holders

Item 6.   Exhibits and Reports on Form 8-K
</TABLE>


<PAGE>   3
                              ECLISPSYS CORPORATION
                      CONDENSED CONSOLIDATED BALANCE SHEETS
                 AS OF SEPTEMBER 30, 1998 AND DECEMBER 31, 1997
                                 (IN THOUSANDS)


<TABLE>
<CAPTION>
                                                              (UNAUDITED)
ASSETS                                                     SEPTEMBER 30, 1998          DECEMBER 31, 1997
                                                           ------------------          -----------------
<S>                                                               <C>                       <C>
Current assets:
Cash and cash equivalents                                           $ 12,309                    $ 4,786
Accounts receivable, net                                              40,443                     30,969
Inventory                                                                539                        866
Other current assets                                                   9,757                      1,114
                                                           ------------------          -----------------
TOTAL CURRENT ASSETS                                                  63,048                     37,735

Fixed assets, net                                                     10,530                      9,517
Capitalized software development costs                                 4,277                      1,591
Acquired technology, net                                              18,798                     25,802
Intangible assets, net                                                15,559                     28,288
Other assets                                                           9,479                      3,832

TOTAL ASSETS                                                       $ 121,691                  $ 106,765
                                                           ==================          =================

LIABILITIES AND SHAREHOLDERS' EQUITY (DEFICIT)
Current liabilities:
Deferred revenue                                                    $ 39,211                   $ 25,295
Current portion of long-term debt                                          -                     12,794
Other current liabilities                                             32,411                     31,150
                                                           ------------------          -----------------
TOTAL CURRENT LIABILITIES                                             71,622                     69,239

Deferred revenue                                                       7,789                      6,966
Long-term debt                                                             -                      3,794
Other long-term liabilities                                            3,713                      9,480

Mandatorily redeemable preferred stock                                     -                     35,607

SHAREHOLDERS' EQUITY (DEFICIT)
Preferred stock                                                            -                         95
Common stock                                                             202                         42
Unearned stock compensation                                             (196)                      (250)
Additional paid-in capital                                           189,341                    115,777
Accumulated other comprehensive income                                    61                         28
Accumulated deficit                                                 (150,841)                  (134,013)
                                                           ------------------          -----------------
TOTAL SHAREHOLDERS' EQUITY (DEFICIT)                                  38,567                    (18,321)


TOTAL LIABILITIES AND SHAREHOLDERS' EQUITY (DEFICIT)               $ 121,691                  $ 106,765
                                                           ==================          =================
</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 THE NINE MONTHS ENDED SEPTEMBER 30, 1998 AND 1997
                (IN THOUSANDS EXCEPT SHARE AND PER SHARE AMOUNTS)
                                  (UNAUDITED)

<TABLE>
<CAPTION>
                                                      THREE MONTHS ENDED                   NINE MONTHS ENDED
                                                         SEPTEMBER 30,                       SEPTEMBER 30,
                                                ------------------------------      -------------------------------
REVENUES                                              1998             1997                1998             1997
                                                      ----             ----                ----             ----
<S>                                              <C>              <C>                 <C>              <C>     
Systems and services                                $ 32,452         $ 23,924            $ 88,541         $ 64,470
Hardware                                               3,708            1,643               9,202            3,009
                                                -------------    -------------      --------------    -------------
TOTAL REVENUES                                        36,160           25,567              97,743           67,479
                                                =============    =============      ==============    =============

COSTS AND EXPENSES
Cost of systems and services revenues                 18,792           19,334              53,196           56,168
Cost of hardware revenues                              3,130            1,062               7,825            2,055
Marketing and sales                                    5,041            3,549              13,945            9,881
Research and development                               6,844            3,964              19,267           11,991
General and administrative                             1,689            1,946               4,580            4,143
Depreciation and amortization                          2,546            2,584               7,937            7,292
Nonrecurring charges                                       -                -               7,193           99,189
                                                -------------    -------------      --------------    -------------
TOTAL COSTS AND EXPENSES                              38,042           32,439             113,943          190,719
                                                -------------    -------------      --------------    -------------

                                                -------------    -------------      --------------    -------------
LOSS FROM OPERATIONS                                  (1,882)          (6,872)            (16,200)        (123,240)
                                                -------------    -------------      --------------    -------------

Interest expense, net                                    124              394                 628              727

                                                -------------    -------------      --------------    -------------
NET LOSS                                              (2,006)          (7,266)            (16,828)        (123,967)
                                                =============    =============      ==============    =============

DIVIDENDS AND ACCRETION ON MANDATORILY
REDEEMABLE PREFERRED STOCK                            (8,415)          (1,611)            (10,928)          (4,199)

PREFERRED STOCK CONVERSION                                 -                -                   -           (3,105)
                                                -------------    -------------      --------------    -------------

NET LOSS AVAILABLE TO COMMON SHAREHOLDERS          $ (10,421)        $ (8,877)          $ (27,756)      $ (131,271)
                                                =============    =============      ==============    =============

BASIC AND DILUTED NET LOSS PER COMMON SHARE          $ (0.70)         $ (2.35)            $ (3.41)        $ (38.28)
                                                =============    =============      ==============    =============

WEIGHTED AVERAGE COMMON SHARES OUTSTANDING        14,934,619        3,771,050           8,133,275        3,429,385
                                                =============    =============      ==============    =============
</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, 1998 AND 1997
                                 (IN THOUSANDS)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                                 NINE MONTHS ENDED SEPTEMBER 30,
                                                                               ------------------------------------

                                                                                    1998                 1997
                                                                               --------------       ---------------
OPERATING ACTIVITIES
<S>                                                                                <C>                  <C>        
Net Loss                                                                           $ (16,828)           $ (123,967)
Adjustments to reconcile net loss to net cash
provided by operating activities
        Depreciation and amortization                                                 20,155                23,156
        Provision for bad debts                                                          750                   450
        Loss on disposal of fixed assets                                                   8                   570
        Write off of in-process research and development and other
        non-recurring charges                                                          7,193                99,189
        Stock compensation expense                                                        54                   151
        Changes in operating assets and liabilities, net of acquisitions
        Accounts receivable                                                           (5,295)                 (505)
        Inventory                                                                        327                   137
        Other current assets                                                           1,025                  (475)
        Other assets                                                                     (81)                  681
        Deferred revenue                                                               9,689                (1,772)
        Other current liabilities                                                     (1,756)                3,986
        Other liabilities                                                                (65)                1,691
                                                                               --------------       ---------------
                  Total adjustments to reconcile net loss to net
                  cash provided by operating activities                               32,004               127,259
                                                                               --------------       ---------------
                          NET CASH PROVIDED BY OPERATING ACTIVITIES                   15,176                 3,292
                                                                               ==============       ===============

INVESTING ACTIVITIES
Purchase of fixed assets, net                                                         (3,573)               (2,097)
Capitalized software development costs                                                (2,686)                 (698)
Acquisitions, net of cash acquired                                                         -              (108,983)
Changes in other assets                                                              (21,565)                    -
                                                                               --------------       ---------------
                          NET CASH USED IN INVESTING ACTIVITIES                      (27,824)             (111,778)
                                                                               ==============       ===============

FINANCING ACTIVITIES
Borrowings                                                                            18,500                10,000
Payments on borrowings                                                               (35,088)                    -
Exercise of stock options                                                                453                     -
Sale of common stock                                                                  66,044
Sale of preferred stock                                                                9,000                73,764
(Redemption)/sale of mandatorily redeemable preferred stock                          (38,771)               30,000
                                                                               --------------       ---------------
                          NET CASH PROVIDED BY FINANCING ACTIVITIES                   20,138               113,764
                                                                               ==============       ===============

EFFECT OF EXCHANGE RATE CHANGES ON CASH AND
   CASH EQUIVALENTS                                                                       33                    21
                                                                               ==============       ===============

NET INCREASE IN CASH AND CASH EQUIVALENTS                                              7,523                 5,299

CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD                                         4,786                 4,589
                                                                               --------------       ---------------
CASH AND CASH EQUIVALENTS, END OF PERIOD                                            $ 12,309               $ 9,888
                                                                               ==============       ===============
</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 (UNAUDITED)
                               SEPTEMBER 30, 1998

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 indicated. All such adjustments are
       considered of normal recurring nature. Quarterly results of operations
       are not necessarily indicative of annual results.

       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 condensed
       consolidated financial statements should be read in conjunction with the
       consolidated financial statements and the notes thereto included in the
       Company's Registration Statement on Form S-1 as amended dated August 6,
       1998.

2.     ACQUISITION
       Effective January 30, 1998, Eclipsys Corporation ("the Company") acquired
       the net assets of the North American operations of Emtek Healthcare
       Systems ("Emtek"), a division of Motorola, Inc. ("Motorola") for an
       aggregate purchase price of $11.7 million, including 1,000,000 shares of
       common stock valued at $9.1 million and liabilities assumed of
       approximately $12.3 million. In addition, Motorola agreed to pay the
       Company $9.6 million in cash due within one year for working capital
       purposes.

       Unaudited pro forma results of operations as if the aforementioned
       acquisition had occurred on January 1, 1998 is as follows (in thousands
       except per share data):
     
<TABLE>
<CAPTION>
                                                                                 NINE MONTHS
                                                     YEAR ENDED                     ENDED
                                                  DECEMBER 31, 1997          SEPTEMBER 30, 1998
                                                  -----------------          ------------------

<S>                                                  <C>                          <C>     
            Revenues                                 $ 116,815                    $ 98,723
            Net loss                                  (153,789)                    (18,518)
            Basic and diluted loss per share           $(35.97)                     $(3.57)
</TABLE>

3.     SIMIONE INVESTMENT
       In April 1998, the Company made a strategic investment in Simione Central
       Holidngs, Inc. ("Simione") a publicly traded company, purchasing 420,000
       shares of restricted common stock from certain stockholders of Simione
       for $5.6 million. At the time of the transaction, the common stock
       represented 4.9% of Simione's outstanding common stock. The Company
       accounts for its investment in these shares using the cost method. Since
       the date of the investment, the market price of Simione's common stock
       has declined. Currently, Management is evaluating whether there has been
       a permanent impairment of this investment in light of market conditions
       and other factors.

       Concurrent with the investment, the Company and Simione entered into a
       remarketing agreement pursuant to which the Company has certain rights to
       distribute Simione software products.


<PAGE>   7


4.     INITIAL PUBLIC OFFERING
       Effective August 6, 1998, the Company completed an initial public
       offering. Net proceeds from the offering were $66.0 million, including
       proceeds from the exercise of the underwriters' over-allotment option.
       The Company used the net proceeds from the offering to redeem the
       outstanding shares of the Company's mandatorily redeemable preferred
       stock, repay the principal balance and accrued interest on acquisition
       related debt and to repay amounts outstanding under the Company's
       revolving credit facility.

       Concurrent with the initial public offering, all classes of preferred
       stock were converted to common stock.

5.     SUBSEQUENT EVENT
       On October 29, 1998, the Company entered into a merger agreement to
       acquire Transition Systems, Inc. ("TSI") for approximately $270.0 million
       in stock. Under the terms of the agreement, each share of TSI stock will
       be converted using a fixed exchange rate of .525 shares of the Company's
       stock, with no collar. The transaction, which is subject to regulatory as
       well as stockholder approval, will be accounted for as a pooling of
       interests and is anticipated to close by the end of January 1999.


<PAGE>   8


       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
       forgoing, the words "believes," "anticipates," "plans," "expects," 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 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 four critical areas - clinical management,
       access management, patient financial management and enterprise data
       warehouse and analysis. These products can be purchased in combination to
       provide an enterprise-wide solution or individually to address specific
       needs. These solutions take many forms and can include a combination of
       software, hardware, maintenance, consulting services, remote processing
       services, network services and information technology outsourcing.

       The Company was formed in December 1995, but had no significant
       operations until January 1997, when it acquired ALLTEL Healthcare
       Information Services, Inc. ("Alltel"). The Company has grown primarily
       through three strategic acquisitions. The Company acquired Alltel
       effective January 24, 1997, SDK Healthcare Information Systems ("SDK")
       effective June 26, 1997 and Emtek effective January 30, 1998,
       (collectively the "Acquisitions"). The Acquisitions were accounted for as
       purchases; accordingly, the Company's consolidated financial statements
       reflect the results of operations of these businesses from the respective
       dates acquired.

       RESULTS OF OPERATIONS

       SUMMARY
       Total revenues for the quarter ended September 30, 1998 increased 41% to
       $36.2 million compared with $25.6 million for the third quarter 1997. For
       the nine months ended September 30, 1998, total revenues increased 45% to
       $97.7 million versus $67.5 million in the same period last year.

       Total costs and expenses for the quarter ended September 30, 1998
       increased 17% compared to the same period in 1997. For the nine months
       ended September 30, 1998, total costs and expenses decreased 40% compared
       to the same period in 1997.

       These changes in revenue and expense combined to decrease net loss for
       the quarter and the nine months ended September 30, 1998 by 72% to ($2.0)
       million and 86% to ($16.8) million, respectively, compared to the same
       periods in 1997.

       Included in the reported quarterly net losses were acquisition related
       amortization of intangible


<PAGE>   9

       assets recorded in connection with the Acquisitions of $4.9 million in
       the third quarter 1998 and $7.0 million in the third quarter 1997.
       Included in the reported year-to-date net losses were acquisition related
       in-process research and development write-offs, amortization of
       intangible assets recorded in connection with the Acquisitions and
       certain non-recurring charges of $22.3 million in the nine months ended
       September 30, 1998 and $117.2 million in the same period in 1997.

       REVENUES
       System and services revenues increased 36% to $32.5 million for the third
       quarter of 1998 and 37% to $88.5 million for the nine months ended
       September 30, 1998, compared to the same periods in 1997. Contributing to
       this increase was the inclusion of the results of operations of the
       Acquisitions throughout the 1998 periods, as well as new contracted
       business during 1998. The increase in new contracted business was a
       result of an increase in marketing efforts related to the regional
       realignment of the Company's operations completed in 1997 and the
       successful integration of the Acquisitions completed in 1997 and 1998.

       Hardware revenues increased 126% to $3.7 million for the third quarter of
       1998 and 206% to $9.2 million for the nine months ended September 30,
       1998, compared to the same periods in 1997. The increase is primarily due
       to increased volume as a result of the Acquisitions and new contracted
       business.

       EXPENSES
       Total cost of revenues increased 7% for the third quarter of 1998 and
       increased 5% for the nine months ended September 30, 1998, compared to
       the same periods in 1997. Increased costs of hardware associated with the
       growth in hardware sales were offset by a reduction of certain expenses
       and realization of cost savings during 1998 as a result of the
       integration of the Acquisitions.

       Marketing and sales expenses increased 42% for the third quarter of 1998
       and 41% for the nine months ended September 30, 1998, compared to the
       same periods in 1997. The increase was primarily due to the addition of
       marketing and direct sales personnel following the Acquisitions and the
       regional realignment of the Company's sales force.

       Total expenditures for research and development, including both
       capitalized and non-capitalized expense increased 73% to $7.7 million for
       the third quarter 1998 and increased 73% to $22.0 million for the nine
       months ended September 30, 1998, compared to the same periods in 1997.
       The increase was due primarily to the inclusion in 1998 of the
       Acquisitions and the continued development of an enterprise-wide, client
       server platform solution. Research and development expenses capitalized
       for the third quarter of 1998 and the nine months ended September 30,
       1998 increased $366,000 and $2.0 million, respectively, compared to the
       same periods in 1997. Increased capitalization is primarily the result of
       projects related to the development of an enterprise-wide, client server
       platform solution.

       General and administrative expenses decreased 13% for the third quarter
       of 1998 and increased 11% for the nine months ended September 30, 1998,
       compared to the same periods in 1997. The quarter decrease is primarily
       the result of certain integration expenses related to the SDK acquisition
       incurred during 1997 that did not occur during 1998. The nine months
       increase is primarily due to the addition of administrative and finance
       personnel following the Acquisitions.

       Depreciation and amortization decreased 1% for the third quarter of 1998
       and increased 9% for the nine months ended September 30, 1998, compared
       to the same periods in 1997. The decrease for the quarter is primarily
       the result of a reduction in Alltel related goodwill amortization as a
       result of a write-down of goodwill due to a renegotiation with the former
       owner of Alltel of certain obligations under a management and services
       agreement (the "Alltel Renegotiation") 

<PAGE>   10

       during 1998. The increase in the nine months depreciation and
       amortization is primarily the result of the timing of the Acquisitions
       and increased depreciation on capital expenditures. This increase is
       partially offset by a reduction in Alltel related goodwill amortization
       as a result of the Alltel Renegotiation.

       ACQUIRED IN-PROCESS RESEARCH AND DEVELOPMENT

       In connection with the Alltel and SDK acquisitions, the Company wrote off
       acquired in-process research and development totaling $92.2 million and
       $7.0 million, 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, 1998, revenues and operating profit attributable to
       acquired in-process research and development have not materially differed
       from the projections used in determining its value, except for, as
       previously reported, the timing of one outsourcing contract. Management
       continues to believe the projections used reasonably estimate the future
       benefits attributable to the acquired in-process research and
       development. However, no assurance can be given that deviations from
       these projections will not occur.

       YEAR 2000 ISSUES

       The Company believes that all of its 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. Although all of the products currently offered by
       the Company are Year 2000 compliant, some of the products previously sold
       by Alltel and Emtek and installed in the Company's customer base are not
       Year 2000 compliant. The Company has developed and tested solutions for
       these non-compliant installed products. The Company currently estimates
       that the total cost of bringing these installed products into Year 2000
       compliance, in those cases in which the Company is required to do so at
       its own expense, will be approximately $900,000, all of which is expected
       to be incurred by mid-1999. In addition, because the Company's products 
       are often interfaced with a customer's existing third-party applications,
       the Company's products may experience difficulties interfacing with 
       third-party non-compliant applications. Any unexpected difficulties in 
       implementing Year 2000 solutions for the installed Alltel or Emtek 
       products or difficulties in interfacing with third-party products could 
       have a material adverse effect on the Company's business, financial 
       condition and results of operations.

       As a result of apprehension in the marketplace over Year 2000 compliance
       issues, businesses, including the Company's customers, may elect to defer
       significant capital investments in information technology programs and
       software, 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. As a result, the Company may not
       achieve expected sales revenues and its business, financial condition and
       results of operations could be materially adversely affected.


<PAGE>   11

       BALANCE SHEET

       INITIAL PUBLIC OFFERING
       Effective August 6, 1998, Eclipsys completed an initial public offering.
       Net proceeds from the offering were $66.0 million, including proceeds
       from the exercise of the underwriters' over-allotment option. The Company
       used the net proceeds from the offering to redeem the outstanding shares
       of the Company's mandatorily redeemable preferred stock, repay the
       principal balance and accrued interest on acquisition related debt and to
       repay amounts outstanding under the Company's revolving credit facility.

       Concurrent with the initial public offering, all classes of preferred
       stock were converted to common stock.

       OTHER CURRENT ASSETS
       Other current assets increased during the nine months ended September 30,
       1998 primarily related to prepaid royalty fees, software maintenance and
       a receivable from Motorola of $9.6 million (as of acquisition date) that
       is due within one year for working capital purposes.

       INTANGIBLE ASSETS
       Intangible assets decreased during the nine months ended September 30,
       1998 primarily due to the Alltel Renegotiation and amortization during
       the period. In connection with the Alltel Renegotiation, the Company
       recorded a reduction of $9.2 million to goodwill. As a result of this
       transaction, the Company recorded a nonrecurring charge of $7.2 million.

       OTHER ASSETS
       Other assets increased during the nine months ended September 30, 1998
       primarily due to a strategic minority investment in Simione, purchasing
       approximately 4.9% of Simione's outstanding common stock from certain
       stockholders of Simione for $5.6 million.

       RECENT DEVELOPMENTS
       On October 29, 1998, the Company entered into a merger agreement to
       acquire Transition Systems, Inc. ("TSI") for approximately $270.0 million
       in stock. Under the terms of the agreement, each share of TSI stock will
       be converted using a fixed exchange rate of .525 shares of the Company's
       stock, with no collar. The transaction, which is subject to regulatory as
       well as stockholder approval, will be accounted for as a pooling of
       interests and is anticipated to close by the end of January 1999.

       LIQUIDITY AND CAPITAL RESOURCES

       During the nine months ended September 30, 1998, the Company generated
       $15.2 million in cash flow from operations. The Company used $27.8
       million in investing activities, which was primarily the result of the
       payment related to the Alltel Renegotiation and the investment in
       Simione. Financing activities provided an additional $20.1 million,
       primarily due to the initial public offering partially offset by the
       redemption of the mandatorily redeemable preferred stock, the repayment
       of the acquisition related debt and the repayment of the amounts
       outstanding under the Company's revolving credit facility.

       As of September 30, 1998, the Company had no outstanding borrowings under
       its $50.0 million revolving credit facility.

       As of September 30, 1998, the Company had $12.3 million in cash and
       short-term investments.

       Management believes that its available cash and short-term investments,
       anticipated cash generated from its future operations and amounts
       available under the existing revolving credit


<PAGE>   12

       facility will be sufficient to meet the Company's operating requirements
       for at least the next twelve months.



<PAGE>   13


       PART II.


       ITEM 2. CHANGES IN SECURITIES AND USE OF PROCEEDS
       The Company is furnishing the following information with respect to the
       use of proceeds from its initial public offering of common stock, $.01
       par value per share, which closed in August 1998.

       1.   The effective date of the Registration Statement on Form S-1 for the
            offering was August 6, 1998, and the commission file number of the
            Registration Statement is 333-50781.

       2.   The offering commenced on August 6, 1998.

       3.   Not applicable

       4.   (i.) The offering terminated on August 17, 1998, the date of the
            exercise of the underwriters' over-allotment option. All of the
            shares of common stock registered for the account of the Company 
            were sold prior to the termination of the offering.
            
            (ii.)     The managing underwriters for the offering were Morgan
                      Stanley Dean Witter, Bancamerica Robertson Stephens, 
                      Lehman Brothers and Salomon Smith Barney.

            (iii.)     The Company registered shares of its common stock, $.01
                      par value per share, in the offering.

            (iv.)      The Company registered 4,830,000 shares. The aggregate
                      offering price of the shares registered and sold by the 
                      Company was $72,450,000

            (v.)      The actual expenses incurred for the account of the
                      Company in connection with the offering were as follows
                      (amounts represent estimates except for Underwriters 
                      discount):

<TABLE>
<S>                                                                   <C>        
                         Underwriting discount                        $ 5,071,500
                         SEC registration fee                              40,000
                         NASD filing fee                                   10,000
                         NASDAQ National Market listing fee               105,000
                         Transfer Agent and Registrar fees                 10,000
                         Accounting fees and expenses                     400,000
                         Legal fees and expenses                          450,000
                         Printing and mailing expenses                    415,000
                         Other                                            270,000
                                                                      -----------
                                                                      $ 6,771,500
</TABLE>

                         Payment of expenses were to persons other than 
                         directors, officers, general partners of the Company
                         or their associates, persons owning 10% or more of
                         the equity securities of the Company or affiliates
                         of the Company.

            (vi.)     The net offering proceeds to the Company after expenses 
                      were approximately $66.0 million. 

            (vii.)    The Company used the proceeds as follows:

<TABLE>
<S>                                                                                 <C>        
                         Redemption of mandatorily redeemable preferred stock        $38,771,443
                         Repayment of acquisition related debt                         3,926,405
                         Repayment of amounts outstanding under revolving
                                credit facility                                       18,500,000
                         Purchase of short-term investments, net of working 
                                capital requirements                                  4,846,152
                                                                                   -------------
                         -----
                                                                                     $66,044,000
</TABLE>

            (viii.)      Not applicable


<PAGE>   14

       ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS
       During the quarter ended September 30, 1998, the Company submitted to a
       vote of its stockholders through the solicitation of written consents
       under Section 128 of the General Corporation Law of the State of Delaware
       the proposal to remove Jeffrey Fox from the Board of Directors. Written
       consents dated August 5, 1998 were received from stockholders. A total of
       13,426,243 votes (out of 17,497,368 shares eligible to vote on the
       matter) were cast in favor of the proposal to remove Mr. Fox from the
       Board of Directors. The share numbers do not reflect the two-for-three
       stock split that occurred subsequent to the stockholder vote.


       ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K
       (a) Exhibits: See Index to exhibits.
       (b) Reports on Form 8-K: Filed with the Securities and Exchange
           Commission on October 30, 1998


<PAGE>   15




                                   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 16, 1998               
                                         ----------------------------
                                              Robert J. Vanaria
                                              Chief Financial Officer


<PAGE>   16



                              ECLIPSYS CORPORATION
                                  EXHIBIT INDEX

       EXHIBIT
          NO.                      DESCRIPTION
       -------                     -----------

       2        Agreement and Plan of Merger
       27       Financial Data Schedule (for SEC use only).