<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, 2000

                        COMMISSION FILE NUMBER: 000-24539



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


<TABLE>
<CAPTION>
<S>                                                                                    <C>
                       DELAWARE                                                                      65-0632092
               (State of Incorporation)                                                 (IRS Employer Identification Number)
</TABLE>


                            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>

<S>                                                                   <C>
                            CLASS                                      SHARES OUTSTANDING AS OF OCTOBER 27, 2000
                            -----                                      -----------------------------------------
                Common Stock, $.01 par value                                           36,999,537
                                                                                       ----------
</TABLE>

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




<PAGE>   2



                              ECLIPSYS CORPORATION

                                    FORM 10-Q

                    FOR THE QUARTER ENDED SEPTEMBER 30, 2000

                                      INDEX

<TABLE>
<S>               <C>
PART I.            Financial Information

Item 1.            Condensed Consolidated Balance Sheets (unaudited) - As of September 30, 2000 and December 31, 1999

                   Condensed Consolidated Statements of Operations (unaudited) - For the Three and Nine Months ended
                   September 30, 2000 and 1999

                   Condensed Consolidated Statements of Cash Flows (unaudited) - For the Nine Months ended
                   September 30, 2000 and 1999

                   Notes to Condensed Consolidated Financial Statements (unaudited) - For the Three and Nine Months ended
                   September 30, 2000 and 1999

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

PART II.           Other Information

Item 2.            Changes in Securities

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




                                       2
<PAGE>   3


PART I.

ITEM 1.

                              ECLIPSYS CORPORATION
                      CONDENSED CONSOLIDATED BALANCE SHEETS
           (UNAUDITED) AS OF SEPTEMBER 30, 2000 AND DECEMBER 31, 1999
                                 (IN THOUSANDS)


<TABLE>
<CAPTION>
                                                                                      SEPTEMBER 30, 2000         DECEMBER 31, 1999
                                                                                      ------------------         -----------------
<S>                                                                                     <C>                        <C>
                   ASSETS
                   Current assets:
                     Cash and cash equivalents                                           $    17,900                $    33,956
                     Accounts receivable, net                                                 63,739                     77,254
                     Inventory                                                                   437                        660
                     Other current assets                                                     10,096                     11,800
                                                                                         -----------                -----------
                   Total current assets                                                       92,172                    123,670

                   Fixed assets, net                                                          15,697                     14,522
                   Capitalized software development costs, net                                10,836                      7,944
                   Acquired technology, net                                                   23,993                     33,161
                   Intangible assets, net                                                     10,077                     16,858
                   Other assets                                                                8,286                      6,780

                                                                                        ------------               ------------
                   TOTAL ASSETS                                                          $   161,061                $   202,935
                                                                                         ===========                ===========

                   LIABILITIES AND STOCKHOLDERS' EQUITY
                   Current liabilities:
                     Deferred revenue                                                    $    45,294                $    49,279
                     Current portion of long-term debt                                           551                          -
                     Other current liabilities                                                30,865                     41,288
                                                                                         -----------                -----------
                   Total current liabilities                                                  76,710                     90,567

                   Deferred revenue                                                            5,083                      8,803
                   Long-term debt                                                              1,177                          -
                   Other long-term liabilities                                                 1,870                      2,264

                   STOCKHOLDERS' EQUITY
                     Common stock                                                                368                        363
                     Unearned stock compensation                                                (212)                      (320)
                     Additional paid-in capital                                              257,336                    254,085
                     Accumulated other comprehensive loss                                       (243)                      (327)
                     Accumulated deficit                                                    (181,028)                  (152,500)
                                                                                         ------------               ------------
                   Total stockholders' equity                                                 76,221                    101,301

                                                                                         ------------               ------------
                   TOTAL LIABILITIES AND STOCKHOLDERS' EQUITY                            $   161,061                $   202,935
                                                                                         ============               ============
</TABLE>


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




                                       3
<PAGE>   4


                              ECLIPSYS CORPORATION
                 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
         FOR THE THREE AND NINE MONTHS ENDED SEPTEMBER 30, 2000 AND 1999
                     (IN THOUSANDS EXCEPT PER SHARE AMOUNTS)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                             THREE MONTHS ENDED            NINE MONTHS ENDED
                                                                               SEPTEMBER 30,                 SEPTEMBER 30,
                                                                       ------------------------------------------------------------
<S>                                                                       <C>             <C>           <C>           <C>
                                                                            2000            1999          2000          1999
                                                                            ----            ----          ----          ----
REVENUES
  Systems and services                                                      $  47,882      $   58,361    $ 153,697      $168,097
  Hardware                                                                      2,731           6,469        8,736        15,937
                                                                             ----------     -----------  -----------    --------
TOTAL REVENUES                                                                 50,613          64,830      162,433       184,034

COSTS AND EXPENSES
  Cost of systems and services revenues                                        40,707          32,168      108,799        93,375
  Cost of hardware revenues                                                     2,167           5,408        6,968        13,421
  Marketing and sales                                                           9,947           9,587       29,143        26,150
  Research and development                                                      9,208          10,055       28,102        34,149
  General and administrative                                                    3,316           2,929        8,231         9,033
  Depreciation and amortization                                                 3,781           4,063       11,107        11,734
  Stock compensation charge                                                         -             982            -         1,987
  Restructuring charge                                                          1,198           1,774        1,198         5,133
  Pooling and transaction costs                                               (1,200)               -        1,900         1,648
                                                                             ----------     -----------  -----------    --------
TOTAL COSTS AND EXPENSES                                                       69,124          66,966      195,448       196,630
                                                                             ----------     -----------  -----------    --------
LOSS FROM OPERATIONS                                                         (18,511)         (2,136)     (33,015)      (12,596)
Interest income, net                                                              223             337          891           945
Other income, net                                                                   -               -        3,596             -
NET LOSS                                                                   $ (18,288)      $  (1,799)    $(28,528)     $(11,651)
                                                                             ==========     ===========  ===========    ========

 BASIC AND DILUTED NET LOSS PER COMMON SHARE                               $   (0.50)      $   (0.05)    $  (0.78)     $  (0.34)
                                                                             ==========     ===========  ===========    ========

 BASIC AND DILUTED WEIGHTED AVERAGE COMMON SHARES OUTSTANDING
                                                                               36,829          35,479       36,672        34,575
                                                                             ----------     -----------  -----------    --------

</TABLE>


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




                                       4
<PAGE>   5


                              ECLIPSYS CORPORATION
                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
              FOR THE NINE MONTHS ENDED SEPTEMBER 30, 2000 AND 1999
                                 (IN THOUSANDS)
                                   (UNAUDITED)

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

                                                                                                  2000                1999
                                                                                               ----------          ----------

<S>                                                                                          <C>              <C>
 OPERATING ACTIVITIES
 Net Loss                                                                                      $ (28,528)        $  (11,651)
 Adjustments to reconcile net loss to net cash
   provided by (used in) operating activities:
             Depreciation and amortization                                                         27,019             31,747
             Provision for bad debts                                                                2,705              1,576
             Write down of accounts receivable                                                      9,400                  -
             Gain on sale of investment                                                           (4,462)                  -
             Write down of investments                                                                802                  -
             Write off of capitalized software development costs                                        -              2,790
             Stock compensation expense                                                               108              2,250
             Changes in operating assets and liabilities, net of acquisitions:
               Accounts receivable                                                                    262            (6,231)
               Inventory                                                                            (102)                 91
               Other current assets                                                                 2,900            (1,447)
               Other assets                                                                       (2,444)                289
               Deferred revenue                                                                   (8,762)            (8,406)
               Other current liabilities                                                         (13,679)            (6,340)
               Other liabilities                                                                    (394)                (5)
                                                                                               ----------         ----------

                        Total adjustments to reconcile net loss to net
                        cash (used in) provided by operating activities                            13,353             16,314
                                                                                               ----------         ----------
                             NET CASH (USED IN) PROVIDED BY OPERATING ACTIVITIES                 (15,175)              4,663
                                                                                               ----------         ----------

 INVESTING ACTIVITIES
   Purchase of fixed assets                                                                       (5,571)            (5,698)
   Purchase of investments                                                                        (7,905)                  -
   Sale or maturity of investments                                                                 12,432             17,003
   Capitalized software development costs                                                         (4,905)            (4,847)
   Acquisitions, net of cash acquired                                                                   -           (25,000)
   Proceeds from sale of business                                                                       -              5,000
                                                                                               ----------         ----------
                             NET CASH USED IN INVESTING ACTIVITIES                                (5,949)           (13,542)
                                                                                               ----------         ----------

 FINANCING ACTIVITIES
   Borrowings                                                                                       2,012             20,000
   Payments on borrowings                                                                           (284)           (20,000)
   Exercise of stock options                                                                        1,760              5,905
   Employee stock purchase plan                                                                     1,492              1,893
   Distributions                                                                                        -              (377)
   Exercise of warrants                                                                                 4                  -
                                                                                               ----------         ----------
                             NET CASH PROVIDED BY FINANCING ACTIVITIES                              4,984              7,421
                                                                                               ----------         ----------

 EFFECT OF EXCHANGE RATES ON CASH AND
      CASH EQUIVALENTS                                                                                 84                 20
                                                                                               ----------         ----------

 NET DECREASE IN CASH AND CASH EQUIVALENTS                                                       (16,056)            (1,438)

 CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD                                                    33,956             37,983
                                                                                               ----------         ----------
 CASH AND CASH EQUIVALENTS, END OF PERIOD                                                      $   17,900         $   36,545
                                                                                               ==========         ==========
 </TABLE>


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




                                       5
<PAGE>   6


                              ECLIPSYS CORPORATION
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
         FOR THE THREE AND NINE MONTHS ENDED SEPTEMBER 30, 2000 AND 1999
                                   (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.

     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 filed March 29, 2000 and as amended April
28, 2000.

2.  ACQUISITIONS

     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.

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

<TABLE>

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

                     Current assets                                  9,830
                     Fixed assets                                      778
                                                                   -------
                                                                    10,608
                                                                   -------
                     Identifiable intangible assets               $ 18,698
                       (acquired technology)                      ========

</TABLE>

     As of March 31, 1999 the Company intended to dispose of Med Data. Effective
July 1, 1999, the Company sold Med Data for $5.0 million in cash. In connection
with the transaction, the Company reduced the acquired technology (disclosed in
the table above) by $4.4 million, which represented the difference between the
sales price and the tangible net assets sold. No gain or loss was recorded.

     During the quarter ended March 31, 2000, the Company finalized the purchase
price allocation related to the Intelus acquisition. As a result, the Company
recorded an increase of $3.3 million to acquired technology (disclosed in the
table above).

     Unaudited pro forma results of operations as if the aforementioned
acquisitions had occurred on January 1, 1999 is as follows (in thousands except
per share data):

<TABLE>
<CAPTION>
                                                                 NINE MONTHS
                                                                ENDED SEPT 30,
                                                                     1999
                                                               ----------------
<S>                                                           <C>
             Revenues                                           $ 187,525
             Net loss                                           $ (12,090)
             Basic and diluted net loss per share               $   (0.35)
</TABLE>

3.   ACCOUNTS RECEIVABLE

     The current portion of unbilled accounts receivable was $13.5 million and
$15.3 million as of September 30, 2000 and December 31, 1999, respectively, and
is included in accounts receivable in the accompanying condensed consolidated
balance sheets. The non-current portion of unbilled accounts receivable was $4.7
million and $1.4 million as of September 30, 2000 and December 31, 1999,
respectively, and is included in other assets in the accompanying condensed
consolidated balance sheets.

                                       6
<PAGE>   7
During the quarter ended September 30, 2000, the Company recorded a charge
totaling $9.4 million in connection with the write down of certain receivables
related to contracts assumed in acquisitions.



4.         INVESTMENTS

     During the quarter ended March 31, 2000, the Company recorded a gain on its
investment in Shared Medical Systems Corp. ("SMS") of approximately $4.5
million. The investment was made in connection with a proposed merger with SMS
that was not consummated. In connection with the proposed merger, the Company
recorded transaction costs of approximately $50,000.

     Additionally, during first quarter 2000, the Company recorded a charge of
approximately $802,000 to write down certain equity securities to their net
realizable value.

5.         TERMINATION OF MERGER

On March 30, 2000, the Company signed an agreement to merge with Neoforma.com,
Inc. ("Neoforma"), a California-based, business-to-business e-commerce services
provider in the medical products, supplies and equipment industry. The merger
was subject to the approval of stockholders of both the Company and Neoforma and
certain other conditions. During the quarter ended June 30, 2000, the Company
and Neoforma agreed to terminate the Merger Agreement without the payment of a
termination fee. Transaction costs incurred in connection with the proposed
merger were approximately $1.9 million.

6.         CHANGES IN SECURITIES

     On July 26, 2000, the Board of Directors of the Company declared a dividend
of one Right for each outstanding share of the Company's Common Stock to
stockholders of record at the close of business on August 9, 2000. Each Right
entitles the registered holder to purchase from the Company one one-thousandth
of a share of Series A Junior Participating Preferred Stock, $.01 par value per
share, at a Purchase Price of $65.00 in cash, subject to adjustment. The Rights
will initially trade together with the Eclipsys Common Stock and will not be
exercisable. If a person or group (other than an exempt person) acquires 15% or
more of the outstanding shares of Eclipsys Common Stock, the Rights generally
will become exercisable and allow the holder (other than the 15% purchaser) to
purchase shares of Eclipsys Common Stock at a 50% discount to the market price.
The effect will be to discourage acquisitions of 15% or more of Eclipsys Common
Stock without negotiations with the Board. The terms of the Rights are set forth
in a Rights Agreement dated as of July 26, 2000 (the "Rights Agreement") between
the Company and Fleet National Bank, as Rights Agent. A copy of the Rights
Agreement has been filed with the Securities and Exchange Commission as an
Exhibit to the Company's Current Report on Form 8-K dated August 8, 2000.

7.         NEW ACCOUNTING PRONOUNCEMENTS

     In March 2000, the Financial Accounting Standards Board issued
Interpretation No. 44 "Accounting for Certain Transactions Involving Stock
Compensation, an interpretation of APB Opinion No. 25" ("FIN 44"). The
interpretation provides guidance for certain issues relating to stock
compensation involving employees that arose in applying APB Opinion No. 25. The
provisions of FIN 44 were effective July 1, 2000. The adoption of FIN 44 has had
no effect on the Company's financial statements.

     In December 1999, the Securities and Exchange Commission ("SEC") issued
Staff Accounting Bulletin No. 101 "Revenue Recognition in Financial Statements"
("SAB No. 101"). SAB No. 101 summarizes certain of the SEC staff's view in
applying generally accepted accounting principles to revenue recognition in
financial statements. On June 26, 2000, the SEC staff issued SAB No. 101-B to
provide registrants with additional time to implement guidance contained in SAB
No. 101. SAB 101-B delays the implementation date of SAB No. 101 until no later
than the fourth fiscal quarter of fiscal years beginning after December 15,
1999. The Company believes its revenue recognition policies are compliant with
the Staff Accounting Bulletin.



                                       7
<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 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 hosting 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 five North American regions.

     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>

     For any acquisitions accounted for using the purchase method of accounting,
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.

                                       8
<PAGE>   9
RESULTS OF OPERATIONS

SUMMARY

     Total revenues for the quarter ended September 30, 2000 decreased 21.9% to
$50.6 million compared with $64.8 million for the third quarter 1999. For the
nine months ended September 30, 2000, total revenues decreased 11.7% to $162.4
million compared to $184.0 million for the same period in 1999.

     Total costs and expenses for the quarter ended September 30, 2000 increased
3.2% compared to the same period in 1999. For the nine months ended September
30, 2000, total costs and expenses decreased 0.6% compared to the same period in
1999.

     These changes in revenues and expenses combined to increase the net loss
for the quarter ended September 30, 2000 by 916.6% to ($18.3) million, compared
to the same period in 1999. Included in the reported quarterly results were
certain acquisition related and non-recurring charges of $16.6 million and $11.1
million for the quarter ended September 30, 2000 and 1999, respectively.

     Year to date changes in revenues and expenses combined to increase net loss
for the nine months ended September 30, 2000 by 144.9% to ($28.5) million
compared to the same period in 1999. Included in the reported nine month net
losses were certain acquisition related and non-recurring charges of $28.6
million and $36.2 million for the nine months ended September 30, 2000 and 1999,
respectively.

REVENUES

     Systems and services revenues decreased 18.0% to $47.9 million for the
third quarter of 2000 compared to the same period in 1999 and 8.6% to $153.7
million for the nine months ended September 30, 2000 compared to the same period
in 1999. The decrease was due to the factors discussed below.

     Prior to 2000, the Company primarily entered into multi-element licensing
arrangements which were accounted for under the percentage-of-completion basis
in which revenues were recognized over the implementation period which typically
ranged from 12 to 24 months where payments for a majority of these contracts
were based on contractual milestones over the term of the implementation. In
2000, the Company began to enter into contracts under multi-element bundled
arrangements that provide for payment terms on a monthly or annual basis over
the term of the contracts which range from 5 to 10 years. Revenue under these
arrangements is generally recognized on a monthly basis over the term of the
agreements. As a result of the change in the Company's business model related to
the new contracting method, the Company experienced a decrease in its revenue in
2000.

     In connection with its prior acquisitions, the Company inherited certain
contracts that were below the Company's normal margins with respect to the cost
of the required implementation services. As a result, revenues were adversely
impacted as the Company continued to honor its commitments under these contracts
which negatively impacted its operating results. To address this problem, the
Company is attempting to increase billings on future work for these customers
and has consolidated its research and development and implementation functions
to reduce costs and enhance the product delivery process.

     In addition, the Company's proposed transactions with SMS and Neoforma.com
resulted in a significant diversion of management's time and attention which
adversely affected revenues.

     The Company's change in its business model and issues associated
with contracts assumed in acquisitions have negatively impacted operating
results to date.  The Company expects to improve its operating results as it
completes its obligations under contracts assumed in prior acquisitions or
increases billings under these contracts.  Additionally, the Company expects
future operating results will improve as it gains market acceptance of its new
business model with respect to new contracts and obtains cost reductions as a
result of the restructure of its implementation and research and development
functions.

     Hardware revenues decreased 57.8% to $2.7 million for the third quarter of
2000 compared to the same period in 1999 and 45.2% to $8.7 million for the nine
months ended September 30, 2000 compared to the same period in 1999. The
decrease was primarily due to decreased volume of hardware sales as a result of
less hardware-intensive transactions.

EXPENSES

     Total cost of revenues increased 14.1% to $42.9 million, or 84.7% of total
revenues, for the third quarter of 2000 compared to the same period in 1999 and
8.4% to $115.8 million, or 71.3% of total revenues, for the nine months ended
September 30, 2000 compared to the same period in 1999. Increased costs of
system and services revenues were partially offset by a decrease in costs of
hardware revenues. Systems and services costs increased as a result of higher
royalty related expenses associated with revenue recognized during the period,
an increased level of outsourcing revenue and associated expenses, and a charge
of $8.7 million during the quarter ended September 30, 2000, to write-down
certain receivables related to contracts assumed in acquisitions. Furthermore,
the Company recorded a charge of $.7 million for other costs related to
finalizing its acquisition integrations. These amounts were offset by decreased
amortization of acquired technology in connection with certain acquisitions done
in prior years.


                                       9
<PAGE>   10
     Marketing and sales expenses increased 3.8% to $9.9 million, or 19.7% of
total revenues, for the third quarter of 2000 compared to the same period in
1999 and 11.4% to $29.1 million, or 17.9% of total revenues, for the nine
months ended September 30, 2000 compared to the same period in 1999. The
increase was primarily due to an increase in commissions as the result of an
increase in new contracted business for the quarter and the nine months ended
September 30, 2000.

     Total expenditures for research and development, including both capitalized
and non-capitalized expenses decreased 4.0% to $11.4 million, or 22.5% of total
revenues, for the third quarter 2000 compared to the same period in 1999 and
10.0% to $35.0 million, or 21.6% of total revenues, for the nine months ended
September 30, 2000 compared to the same period in 1999. The decrease was due
primarily to a 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 in 1999 and the realization of integration synergies.
Research and development expenses capitalized for the third quarter of 2000
decreased $.3 million compared to the same period in 1999 and were relatively
level for the nine months ended September 30, 2000 as compared to the same
period in 1999. The decrease in capitalized research and development expenses
for the quarter ended September 30, 2000 was primarily the result of the
completion of development and release of its Sunrise Clinical Manager product
and certain other products at the end of the first quarter of 2000.

     General and administrative expenses increased 13.2% to $3.3 million, or
6.6% of total revenues, for the third quarter of 2000 compared to the same
period in 1999 and decreased by 8.9% to $8.2 million, or 5.1% of total
revenues, for the nine months ended September 30, 2000 compared to the same
period in 1999. The decrease for the nine months was primarily due to the
Company's restructuring plans that were completed in late 1999 and 2000. This
was partially offset by a $.7 million write-down of receivables during the three
months ended September 30, 2000.

     Depreciation and amortization decreased 6.9% to $3.8 million, or 7.5% of
total revenues, for the third quarter of 2000 compared to the same period in
1999 and 5.3% to $11.1, or 6.8% of total revenues, for the nine months ended
September 30, 2000 compared to the same period in 1999. The decrease is
primarily the result of certain fixed assets becoming fully depreciated,
partially offset by depreciation related to purchases of fixed assets during the
quarter and nine months ended September 30, 2000.

     During the quarter ended June 30, 1999, the Company initiated a
restructuring of its operations. The restructuring was completed during the
quarter ended September 30, 1999 and resulted in a charge totaling $5.1 million
related to the closing of duplicate facilities and the termination of certian
employees.

     During the quarter ended September 30, 2000, the Company initiated and
completed a restructure of its operations. The restructure rationalized
employee headcount following the finalization of its integration of its
acquisitions. Additionally, the Company consolidated its research and
development and implementation functions. Charges in connection with this
restructuring plan totaled $1.2 million.

     Pooling and transaction costs for the third quarter of 2000 reflected a
benefit of ($1.2) million, or (2.4%) of total revenues, compared to $0 for the
same period in 1999 and increased 15.3%  to $1.9 million, or 1.7% of total
revenues, for the nine months ended September 30, 2000 compared to the same
period in 1999. The ($1.2) million benefit in pooling and transaction costs was
the result of the Company's ability to negotiate favorable reductions in certain
costs recorded in the quarter ended March 31, 2000. Pooling and transaction
costs incurred during the quarter and nine months ended September 30, 1999 were
related to the poolings of PowerCenter and MSI. The transaction costs during the
three and nine months ended September 30, 2000, are primarily the result of
costs associated with proposed transactions with Shared Medical Systems Corp.
(SMS) and Neoforma.com, Inc. (Neoforma).

     Other income recorded during the nine months ended September 30, 2000
related to a gain on the Company's investment in SMS during the first quarter of
2000. (See notes to the unaudited condensed consolidated financial statements.)

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.


                                       10
<PAGE>   11
     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, 2000, 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 and during the first
nine months of 2000, 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 and activated certain sites 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.

BALANCE SHEET

ACCOUNTS RECEIVABLE

     Accounts receivable decreased primarily as a result of a charge recorded
in the quarter ended September 30, 2000 related to the write-down of certain
receivables associated with contracts assumed in acquisitions.

CAPITALIZED SOFTWARE DEVELOPMENT COSTS

     Capitalized software development costs increased during the nine months
ended September 30, 2000 primarily due to the continued development of an
enterprise-wide, web-enabled, client server platform solution that had reached
technological feasibility.

ACQUIRED TECHNOLOGY

     Acquired technology decreased during the nine months ended September 30,
2000 primarily due to amortization partially offset by the final purchase price
adjustment for Intelus.

INTANGIBLE ASSETS

     Intangible assets decreased during the nine months ended September 30, 2000
due to amortization.

OTHER ASSETS

     Other assets increased during the nine months ended September 30, 2000
primarily due to higher unbilled revenue under long-term contracts partially
offset by a write-down of its investment in certain equity securities to their
net realizable value.

DEFERRED REVENUE

     Deferred revenue decreased during the nine months ended September 30, 2000
primarily due to revenues earned under certain contractual arrangements.

OTHER CURRENT LIABILITIES

     Other current liabilities decreased during the nine months ended September
30, 2000 primarily due to the timing of certain employee compensation related
expenses.

                                       11
<PAGE>   12
LIQUIDITY AND CAPITAL RESOURCES

     During the nine months ended September 30, 2000, the Company used $15.2
million in operations. Included in operations is approximately $10.5 million of
annual employee compensation related liabilities paid during the first quarter.
Investing activities used $5.9 million for the purchase of fixed assets and the
funding of development costs partially offset by the sale of investments.
Financing activities provided $5.0 million, due to borrowings under an equipment
financing arrangement, exercise of stock options and the employee stock purchase
plan.

     During October 2000, the Company amended its revolving credit facility. The
amendment extended the agreement through May 2002, changed the maximum
borrowings to $30.0 million and revised certain other provisions of the
facility. Under the amended facility, available borrowings are based on accounts
receivable, as defined and certain other criteria. As of September 30, 2000, the
Company's available borrowings under the facility were approximately $16.4
million. There were no outstanding borrowings under the facility as of September
30, 2000.

     As of September 30, 2000, the Company had $17.9 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.



                                       12
<PAGE>   13
PART II.

ITEM 2.  CHANGES IN SECURITIES

     On July 26, 2000, the Board of Directors of the Company declared a dividend
of one Right for each outstanding share of the Company's Common Stock to
stockholders of record at the close of business on August 9, 2000. Each Right
entitles the registered holder to purchase from the Company one one-thousandth
of a share of Series A Junior Participating Preferred Stock, $.01 par value per
share, at a Purchase Price of $65.00 in cash, subject to adjustment. The Rights
will initially trade together with the Eclipsys Common Stock and will not be
exercisable. If a person or group (other than an exempt person) acquires 15% or
more of the outstanding shares of Eclipsys Common Stock, the Rights generally
will become exercisable and allow the holder (other than the 15% purchaser) to
purchase shares of Eclipsys Common Stock at a 50% discount to the market price.
The effect will be to discourage acquisitions of 15% or more of Eclipsys Common
Stock without negotiations with the Board. The terms of the Rights are set forth
in a Rights Agreement dated as of July 26, 2000 (the "Rights Agreement") between
the Company and Fleet National Bank, as Rights Agent. A copy of the Rights
Agreement has been filed with the Securities and Exchange Commission as an
Exhibit to the Company's Current Report on Form 8-K dated August 8, 2000. This
summary does not purport to be complete and is qualified in its entirety by
reference to the Rights Agreement.

ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

     (a) Exhibits: See Index to exhibits.

     (b) Reports on Form 8-K:

          (1)  The Company filed a Current Report on Form 8-K, with the
          Securities and Exchange Commission on August 8, 2000, relating to the
          Rights Agreement dated July 26, 2000 by and between Eclipsys
          Corporation and Fleet National Bank, as Rights Agent.


<PAGE>   14



                                   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.


<TABLE>
<CAPTION>
                                                   ECLIPSYS CORPORATION



<S>                                              <C>
Date:  November 14, 2000                           /s/ GREGORY L. WILSON
                                                   --------------------------------------------------------
                                                   Gregory L. Wilson
                                                   Senior Vice President, Chief Financial Officer and
                                                   Treasurer
</TABLE>


                                       13
<PAGE>   15






                              ECLIPSYS CORPORATION
                                  EXHIBIT INDEX


<TABLE>
<CAPTION>

EXHIBIT
  NO.                                   DESCRIPTION
--------                                -----------
<S>              <C>
   3.1            Certificate of Incorporation, as amended by the Certificate of Designations
                  of Series A Junior Participating Preferred Stock, filed with the Secretary of
                  State of the State of Delaware on August 8, 2000.

  27              Financial Data Schedule (for SEC use only)
</TABLE>


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