ECLIPSYS CORP
S-3/A, 1999-12-21
COMPUTER INTEGRATED SYSTEMS DESIGN
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<PAGE>   1


   AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON DECEMBER 21, 1999


                                            REGISTRATION STATEMENT NO. 333-92251

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

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                               ------------------

                                AMENDMENT NO. 1


                                       TO


                                    FORM S-3
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
                               ------------------

                              ECLIPSYS CORPORATION
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

                                    DELAWARE
                          (STATE OR OTHER JURISDICTION
                       OF INCORPORATION OR ORGANIZATION)

                                   65-0632092
                      (I.R.S. EMPLOYER IDENTIFICATION NO.)

       777 EAST ATLANTIC AVENUE, SUITE 200, DELRAY BEACH, FLORIDA 33483,
                                 (561) 243-1440
  (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
                   REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)
                               ------------------

                                HARVEY J. WILSON
                            CHIEF EXECUTIVE OFFICER
                              ECLIPSYS CORPORATION
        777 EAST ATLANTIC AVENUE, SUITE 200, DELRAY BEACH, FLORIDA 33483
                                 (561) 243-1440
 (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
                        OF AGENT FOR SERVICE OF PROCESS)
                               ------------------
                                   Copies to:
                              BRENT B. SILER, ESQ.
                               HALE AND DORR LLP
             1455 PENNSYLVANIA AVENUE, N.W., WASHINGTON, D.C. 20004
                    TEL: (202) 942-8400, FAX: (202) 942-8484

            APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO PUBLIC:
  As soon as practicable after this Registration Statement becomes effective.

    If the only securities being registered on this Form are being offered
pursuant to dividend or interest reinvestment plans, please check the following
box.  [ ]

    If any of the securities being registered on this Form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box.  [X]

    If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering.  [ ] 333-         .

    If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering.  [ ] 333-          .

    If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box.  [ ]
                               ------------------
     THE COMPANY HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR DATES
AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE COMPANY SHALL FILE A
FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION STATEMENT
SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF THE
SECURITIES ACT OF 1933 OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(a),
SHALL DETERMINE.

- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
<PAGE>   2


PROSPECTUS


                              ECLIPSYS CORPORATION

                    7,577,285 SHARES OF VOTING COMMON STOCK

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

     Eclipsys Corporation previously issued 3,361,660 shares of its voting
common stock to the former stockholders of PowerCenter Systems, Inc., MSI
Solutions, Inc. and MSI Integrated Services, Inc. in connection with our
acquisition of those companies. In addition, pursuant to the Second Amended and
Restated Registration Rights Agreement, as amended, by and among Eclipsys
Corporation and several of our stockholders, stockholders holding an aggregate
of 4,215,625 shares of voting common stock have elected to include their shares
of voting common stock in this prospectus. This prospectus relates to resales of
these 7,577,285 shares.

     We will not receive any proceeds from the sale of the shares.

     We have agreed to pay certain expenses in connection with the registration
of the shares and to indemnify the selling stockholders against certain
liabilities. The selling stockholders will pay all underwriting discounts and
selling commissions, if any, in connection with the sale of the shares.

     The selling stockholders, or their pledgees, donees, transferees or other
successors in interest, may offer the shares from time to time through public or
private transactions at prevailing market prices, at prices related to
prevailing market prices or at privately negotiated prices.


     Our common stock is traded on the Nasdaq National Market under the symbol
"ECLP." On December 20, 1999, the closing sale price of the common stock on
Nasdaq was $25.625 per share.


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

     INVESTING IN OUR VOTING COMMON STOCK INVOLVES A HIGH DEGREE OF RISK. SEE
"RISK FACTORS" BEGINNING ON PAGE 4.

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

     THE SECURITIES AND EXCHANGE COMMISSION AND STATE SECURITIES REGULATORS HAVE
NOT APPROVED OR DISAPPROVED OF THESE SECURITIES OR DETERMINED WHETHER THIS
PROSPECTUS IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.

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


               The date of this prospectus is December 21, 1999.

<PAGE>   3

                               TABLE OF CONTENTS


<TABLE>
<CAPTION>
                                                              PAGE
                                                              ----
<S>                                                           <C>
Prospectus Summary..........................................    3
Risk Factors................................................    4
Special Note Regarding Forward-Looking Information..........   10
Use of Proceeds.............................................   10
Selling Stockholders........................................   11
Plan of Distribution........................................   15
Legal Matters...............................................   16
Experts.....................................................   16
Where You Can Find More Information.........................   17
Incorporation of Certain Documents By Reference.............   17
</TABLE>


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

     Our executive offices are located at 777 East Atlantic Avenue, Suite 200,
Delray Beach, Florida 33483, our telephone number is (561) 243-1440 and our
Internet address is http://www.eclipsys.com. The information on our Internet
website is not incorporated by reference in this prospectus. Unless the context
otherwise requires references in this prospectus to "Eclipsys," "we," "us," and
"our" refer to Eclipsys Corporation and its subsidiaries.

     We have not authorized anyone to provide you with information different
from that contained or incorporated by reference in this prospectus. The selling
stockholders are offering to sell, and seeking offers to buy, shares of our
voting common stock only in jurisdictions where offers and sales are permitted.
The information contained in this prospectus is accurate only as of the date of
this prospectus, regardless of the time of delivery of this prospectus or of any
sale of voting common stock.

                                       -2-
<PAGE>   4

                               PROSPECTUS SUMMARY

     This summary highlights important features of this offering and the
information included or incorporated by reference in this prospectus. This
summary does not contain all of the information that you should consider before
investing in our voting common stock. You should read the entire prospectus
carefully, especially the risks of investing in our voting common stock
discussed under "Risk Factors."

                              ECLIPSYS CORPORATION

     Eclipsys is a healthcare information technology company delivering
solutions that enable healthcare providers to achieve improved clinical,
financial and satisfaction outcomes. We offer an integrated suite of healthcare
products and associated services 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 and services can be licensed
either in combination to provide an enterprise-wide solution or individually to
address specific needs.

     Our products and services have been designed for the purpose of delivering
a measurable impact on outcomes, enabling our customers to quantify clinical
benefits and return on investment in a precise and timely manner. Our products
can be integrated with a customer's existing information systems through web
integration tools, which we believe reduces overall cost of ownership, leverages
existing investment and increases the attractiveness of our products. We also
provide outsourcing, remote processing, web and integration tools and services
and networking services to assist customers in meeting their healthcare
information technology requirements.

     We market our products primarily to large hospitals, academic medical
centers and integrated healthcare delivery networks. We have one or more of our
products installed or being installed in over 1,300 facilities. To provide
direct and sustained customer contact, we maintain decentralized sales,
implementation and customer support teams in each of our eight North American
regions.

     Eclipsys Corporation was formed in December 1995 and has grown primarily
through a series of acquisitions, all completed since January 1997. These
transactions, together with internally generated growth, have resulted in
revenues of $183.4 million in 1998 on a pro forma basis as if the acquisitions
occurred January 1, 1998.

                                  THE OFFERING

Voting common stock offered by
selling stockholders..........   7,577,285 shares

Use of proceeds...............   Eclipsys Corporation will not receive any
                                 proceeds from the sale of shares in this
                                 offering.

Nasdaq National Market
symbol........................   ECLP

                                       -3-
<PAGE>   5

                                  RISK FACTORS

     You should carefully consider the risks described below before you decide
to buy our voting common stock. The risks and uncertainties described below are
not the only ones facing our company. Additional risks and uncertainties may
also impair our business operations.

     If any of the following risks actually occur, our business, financial
condition, or results of operations would likely suffer. In such case, the
trading price of our voting common stock could decline and you could lose all or
part of your investment.

     Limited Operating History of Eclipsys; History of Operating Losses.  We
began operations in 1996 and have grown primarily through a series of eight
acquisitions completed since January 1997. Accordingly, there is only a limited
combined operating history of Eclipsys and its acquired operations upon which to
base an evaluation of Eclipsys and its prospects. We will need to continue to
integrate the operations of the businesses we acquired and to consolidate their
product offerings. We have incurred net losses in each year since our inception,
including net losses of $126.3 million in 1997 and $35.3 million in 1998. These
losses resulted primarily from certain write-offs related to acquisitions we
completed during 1997 and 1998, and charges in the first quarter of 1998 related
to the buyout by us of certain obligations under an agreement entered into in
connection with one of the acquisitions. We expect to continue to incur net
losses for the foreseeable future. We cannot predict when or if we will achieve
profitability.

     Management of Growth.  The rapid growth in the size and complexity of our
business as a result of our acquisitions has placed a significant strain on our
management and other resources. To compete effectively and to manage future
growth, if any, we will need to implement and improve operational and financial
systems on a timely basis and to expand, train, motivate and manage our work
force. Our personnel, systems, procedures and controls may not be adequate to
support our operations.

     Risks Associated with Future Acquisitions.  An important element of our
business strategy has been expansion through acquisitions. We expect to continue
this strategy. This acquisition strategy involves a number of risks, which
include:

     - There is significant competition for acquisition opportunities in the
       healthcare information technology industry. Competition may intensify due
       to consolidation in the industry, which could increase the costs of
       future acquisitions. We will compete for acquisition opportunities with
       other companies, some of which may have significantly greater financial
       and management resources than we have.

     - The anticipated benefits from any acquisition may not be achieved unless
       the operations of the acquired business are successfully combined with
       ours. The integration of acquired businesses requires substantial
       attention from management. The diversion of the attention of management
       and any difficulties encountered in the transition process could hurt us.

     - Future acquisitions could result in the issuance of additional shares of
       capital stock or the incurrence of additional indebtedness, could entail
       the payment of consideration in excess of book value and could have a
       dilutive effect on our net income per share.

     - Many business acquisitions must be accounted for under the purchase
       method of accounting. Consequently, such acquisitions may generate
       significant goodwill or other intangible assets and result in substantial
       amortization charges to us. Acquisitions could also involve significant
       one-time charges. As a result of previous acquisitions, in 1998, we
       recorded amortization expenses for acquisition-related intangible assets
       of $20.9 million, wrote off $2.4 million of in-process research and
       development and recorded a charge of $7.2 million related to the
       write-off of acquisition related intangibles.

                                       -4-
<PAGE>   6

     Potential Fluctuations in Quarterly Performance.  We have experienced
significant variations in revenues and operating results from quarter to
quarter. Our quarterly operating results may continue to fluctuate due to a
number of factors, including:

     - potential deferrals of sales resulting from customer concerns over the
       Year 2000 issue;

     - the timing and size of future acquisitions;

     - the timing, size and nature of our product sales and implementations;

     - the length of the sales cycle;

     - the success of implementation efforts;

     - market acceptance of new services, products or product enhancements by us
       or our competitors;

     - product and price competition;

     - the relative proportions of revenues derived from systems and services
       and from hardware;

     - changes in operating expenses;

     - personnel changes;

     - the performance of our products; and

     - fluctuations in economic and financial market conditions.

     It is difficult to predict the timing of revenues from product sales
because the sales cycle can vary depending upon several factors. These factors
include the size of the transaction, the changing business plans of the
customer, the effectiveness of the customer's management and general economic
conditions. In addition, because revenue is recognized at various points during
the term of a contract, the timing of revenue recognition varies considerably.
Factors affecting the timing of revenue recognition include the type of
contract, the availability of personnel, the implementation schedule and the
complexity of the implementation process. Because a significant percentage of
our expenses will be relatively fixed, a variation in the timing of sales and
implementations could cause significant variations in operating results from
quarter to quarter. We believe that period-to-period comparisons of our
historical results of operations are not necessarily meaningful. You should not
rely on these comparisons as indicators of future performance.

     Long Sales and Implementation Cycles.  We have experienced long sales and
implementation cycles. How and when to implement, replace, expand or
substantially modify an information system, or modify or add business processes
or lines of business, are major decisions for customers. Furthermore, the
license of solutions like those we provide typically require significant capital
expenditures by the customer. The sales cycle for our systems has ranged from 6
to 18 months or more from initial contact to contract execution. Historically,
our implementation cycle has ranged from 6 to 36 months from contract execution
to completion of implementation. Although we believe that the migration of our
products to our new SOLA platform will significantly shorten the implementation
cycle, we cannot provide any assurance in this regard. During the sales cycle
and the implementation cycle, we will expend substantial time, effort and funds
preparing contract proposals, negotiating the contract and implementing the
solution.

     Risks Associated with Our Development of Our Integrated Clinical Management
Suite.  We are currently in the process of integrating selected features and
functionalities from a number of clinical management products acquired in our
mergers and acquisitions and licensed from Partners HealthCare System, Inc.
("Partners"), to create the Sunrise Clinical Manager suite. This product suite
is currently undergoing field trials. Although most of the key functionalities
of the Sunrise Clinical Manager suite are currently available in heritage
products, we do not expect the integrated Sunrise Clinical Manager suite to be
generally available until the end of 1999. We may not be successful in
completing the integration of these functionalities on a timely basis. In
addition, the field trials may not be successful and the Sunrise Clinical

                                       -5-
<PAGE>   7

Manager suite, if and when generally available, may not meet the needs of the
marketplace or achieve market acceptance.

     Competition.  We operate in a market that is intensely competitive. Our
principal competitors include Cerner Corp., McKesson HBOC, Inc., IDX Systems
Corp. and Shared Medical Systems Corporation. We will also face competition from
providers of practice management systems, general decision support and database
systems and other segment-specific applications, as well as from healthcare
technology consultants. A number of existing and potential competitors are more
established and have greater name recognition and financial, technical and
marketing resources than we do. We expect that competition will continue to
increase as a result of consolidation in both the information technology and
healthcare industries.

     Dependence on Relationship with Partners and Other Third Parties.  We have
an exclusive license granted by Partners to develop, commercialize, distribute
and support certain intellectual property relating to clinical information
systems software developed at Brigham and Women's Hospital, Inc. If we breach
certain terms of the license, then Partners has the option to convert the
license to a non-exclusive license. Such conversion by Partners could cause the
intellectual property and the ability to develop and commercialize such
intellectual property to become more widely available to our competitors. We
also work closely with physicians and research and development personnel at BWH
and its affiliate, Massachusetts General Hospital, to develop and commercialize
new information technology solutions for the healthcare industry and to test and
demonstrate new and existing products. If we breach the Partners license, then
the cooperative working relationship with BWH and MGH, including future access
to products developed by personnel at BWH granted under the Partners license,
could become strained or cease altogether. The loss of good relations with BWH
or MGH could hurt our ability to develop new solutions and could cause delays in
bringing new products to the market. In addition, our reputation and status in
the industry could be hurt.

     Additionally, we depend upon licenses for certain technology used in our
products from a number of third-party vendors, including Computer Corporation of
America, Computer Associates, Oracle Corporation and Sterling Software (United
States of America), Inc. We also have licenses from Premier, Inc. for certain
comparative database systems and other software components and clinical
benchmarking data. Most of these licenses expire within one to four years, can
be renewed only by mutual consent and may be terminated if we breach the terms
of the license and fail to cure the breach within a specified period of time. We
may not be able to continue using the technology licensed under these licenses
on commercially reasonable terms or at all. As a result, we may have to
discontinue, delay or reduce product shipments until equivalent technology is
obtained, which could hurt us. Most of our third party licenses, including our
license from New England Medical Center, Inc. for the original version of the
Transition I software, are non-exclusive. Our competitors may obtain the right
to use any of the technology covered by the licenses and use the technology to
directly compete with us. In addition, if our vendors choose to discontinue
support of the licensed technology, we may not be able to modify or adapt our
own products going forward.

     Uncertainty in the Healthcare Industry.  We operate in an industry subject
to changing political, economic and regulatory influences. The potential impact
of these industry changes include:

     - During the past several years, the U.S. healthcare industry has been
       subject to an increase in governmental regulation and reform proposals.
       These reforms may increase governmental involvement in healthcare,
       continue to reduce reimbursement rates and otherwise change the operating
       environment for our customers. Customers may react to these proposals and
       the uncertainty surrounding the proposals by curtailing or deferring
       investments, including those for our products and services.

     - Many healthcare providers are consolidating to create larger healthcare
       delivery enterprises with greater market power. This consolidation could
       erode our customer base and could reduce the size of our target market.
       In addition, the resulting enterprises could have greater bargaining
       power, which may lead to price erosion.
                                       -6-
<PAGE>   8

     Potential FDA Regulation.  The U.S. Food and Drug Administration is likely
to become increasingly active in regulating computer software intended for use
in the healthcare setting. The FDA has increasingly focused on the regulation of
computer products and computer-assisted products as medical devices under the
Federal Food, Drug, and Cosmetic Act. If the FDA chooses to regulate any of our
products as medical devices, it can impose extensive requirements upon us,
including:

     - we would be required to seek either FDA clearance of a pre-market
       notification submission demonstrating that the product is substantially
       equivalent to a device already legally marketed or obtain FDA approval of
       a pre-market approval application establishing the safety and
       effectiveness of the product;

     - we would be required to comply with rigorous regulations governing the
       pre-clinical and clinical testing, manufacture, distribution, labeling
       and promotion of medical devices; and

     - we would be required to comply with the FDC Act's general controls,
       including establishment registration, device listing, compliance with
       good manufacturing practices, reporting of certain device malfunctions
       and adverse device events.

     If we failed to comply with applicable requirements, then the FDA could
respond by imposing fines, injunctions or civil penalties, requiring recalls or
product corrections, suspending production, refusing to grant pre-market
clearance or approval of products, withdrawing clearances and approvals, and
initiating criminal prosecution. Any final FDA policy governing computer
products, once issued, may increase the cost and time to market of new or
existing products.

     New Regulations Relating to Patient Confidentiality.  State and federal
laws regulate the confidentiality of patient records and the circumstances under
which such records may be released. These regulations govern both the disclosure
and use of confidential patient medical records information. Regulations
governing electronic health data transmissions are evolving rapidly and are
often unclear and difficult to apply. On August 22, 1996, President Clinton
signed the Health Insurance Portability and Accountability Act of 1996, or
HIPAA. This legislation requires the Secretary of Health and Human Services, or
HHS, to (i) adopt national standards for certain types of electronic health
information transactions and the data elements used in such transactions, (ii)
adopt standards to ensure the integrity and confidentiality of health
information, and (iii) establish a schedule for implementing national health
data privacy legislation or regulations.

     - The Secretary of HHS recently issued proposed standards regarding four of
       the seven sets of standards that are ultimately expected. The data
       standards which have been proposed are expected to be issued as final
       rules in late 1999, to become effective in 2002. We believe that the
       proposed data standards issued to date would not materially affect our
       business if adopted as proposed. We cannot predict the potential impact
       of the standards that have not yet been proposed or any other standards
       that might be finally adopted instead of the proposed standards.

     - The HIPAA legislation also required the Secretary of HHS to submit to
       Congress recommendations for legislation to protect the privacy and
       confidentiality of personal health information, and the law stated that
       if national privacy legislation was not enacted by August 21, 1999, then
       the Secretary of HHS would be required to issue privacy regulations by
       February 21, 2000. Since privacy legislation has not yet been enacted,
       the Secretary of HHS is now required to issue privacy regulations. In
       addition, federal and/or state privacy legislation may be enacted at any
       time. Such legislation, if enacted, could also require patient consent
       before even non-individually-identifiable (e.g., coded or anonymous)
       patient information may be shared with third parties and could require
       that holders or users of such information implement specified security
       measures. These laws or regulations, when adopted, could restrict the
       ability of customers to obtain, use, or disseminate patient information.
       This could adversely affect demand for our products.

     Year 2000 Issue.  We have a Year 2000 Committee whose task is to evaluate
our Year 2000 readiness for both internal and external management information
systems, recommend a plan of action to minimize disruption and execute our Year
2000 plan. The Committee has developed a comprehensive
                                       -7-
<PAGE>   9

checklist and Year 2000 Plan. The Year 2000 Plan covers the major and minor
internal and external management information systems.

     We believe that our internal management information systems are currently
Year 2000 compliant and, accordingly, do not anticipate any significant
expenditures to remediate or replace existing internal-use systems.

     All of the products currently offered by us are Year 2000 compliant. Some
of the products previously sold by Alltel and Emtek and installed in our
customer base are not Year 2000 compliant. We have developed and tested
solutions for these non-compliant installed products. We currently estimate that
the total cost of bringing these installed products into Year 2000 compliance,
in those cases in which we are required to do so at our own expense, is not
expected to be material.

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

     Unexpected difficulties in implementing Year 2000 solutions for the
installed Alltel or Emtek products or difficulties in interfacing with
third-party products could adversely affect us.

     Apprehension in the marketplace over Year 2000 compliance issues may lead
businesses, including our customers, to defer significant capital investments in
information technology programs and software. They could elect to defer those
investments either because they decide to focus their capital budgets on the
expenditures necessary to bring their own existing systems into compliance or
because they wish to license only software with a proven ability to process data
after 1999. If these deferrals are significant, then we may not achieve expected
revenue or earnings levels.

     Potential for Product Liability; Security Issues.  We provide products with
applications that relate to patient medical histories and treatment plans. If
these products fail to provide accurate and timely information, customers could
assert liability claims against us. We attempt to contractually limit our
liability for damages arising from negligence, errors or mistakes. Despite this
precaution, the limitations of liability set forth in these contracts may not be
enforceable or may not otherwise protect us from liability for damages. We
maintain general liability insurance coverage, including coverage for errors or
omissions. However, such coverage may not continue to be available on acceptable
terms or may not be available in sufficient amounts to cover one or more large
claims. In addition, the insurer might disclaim coverage as to any future claim.
One or more large claims could exceed available insurance coverage. Litigation
with respect to liability claims, regardless of its outcome, could result in
substantial cost to us, could divert management's attention from operations and
could decrease market acceptance of the our products. We have included security
features in our products that are intended to protect the privacy and integrity
of customer data. Despite the existence of these security features, these
products may be vulnerable to break-ins and similar disruptive problems.
Break-ins and other disruptions could jeopardize the security of information
stored in and transmitted through the computer systems of customers. We may need
to expend significant capital and other resources to address evolving security
issues.

     Ability to Attract and Retain Key Personnel.  Our success depends, in
significant part, upon the continued services of our key technical, marketing,
sales and management personnel and on our ability to continue to attract,
motivate and retain highly qualified employees. Competition for technical,
marketing, sales and management employees is intense and the process of
recruiting personnel with the combination of skills and attributes required to
execute our strategy can be difficult, time-consuming and expensive. We believe
that our ability to implement our strategic goals depends to a considerable
degree on our senior management team. The loss of any member of that team or, in
particular, the loss of Harvey J. Wilson, our founder, Chairman of the Board and
member of the Office of the Chairman, could hurt our business.

     Rapid Technological Change and Evolving Market.  The market for our
products and services is characterized by rapidly changing technologies,
evolving industry standards and new product introductions
                                       -8-
<PAGE>   10

and enhancements that may render existing products obsolete or less competitive.
As a result, our position in the healthcare information technology market could
erode rapidly due to unforeseen changes in the features and functions of
competing products, as well as the pricing models for such products. Our future
success will depend in part upon our ability to enhance our existing products
and services and to develop and introduce new products and services to meet
changing customer requirements. The process of developing products and services
such as those offered by us is extremely complex and is expected to become
increasingly complex and expensive in the future as new technologies are
introduced. We have recently announced the development of, and have commenced
migrating our products to, SOLA. We cannot assure you that the development of
SOLA or the migration of products to SOLA will be successful that such products
will meet their scheduled release dates, that we will successfully complete the
development and release of other new products or the migration of new or
existing products to specific platforms or configurations in a timely fashion or
that our current or future products will satisfy the needs of potential
customers or gain general market acceptance.

     Limited Protection of Proprietary Rights.  We are dependent upon our
proprietary information and technology. We cannot assure you that our means of
protecting our proprietary rights will be adequate to prevent misappropriation.
The laws of some foreign countries may not protect our proprietary rights as
fully or in the same manner as do the laws of the United States. Also, despite
the steps we have taken to protect our proprietary rights, it may be possible
for unauthorized third parties to copy aspects of our products, reverse engineer
such products or otherwise obtain and use information that we regard as
proprietary. In certain limited instances, customers can access source code
versions of our software, subject to contractual limitations on the permitted
use of such source code. Although our license agreements with such customers
attempt to prevent misuse of the source code, the possession of our source code
by third parties increases the ease and likelihood of potential misappropriation
of such software. Furthermore, there can be no assurance that others will not
independently develop technologies similar or superior to our technology or
design around the our proprietary rights. In addition, although we do not
believe that our products infringe the proprietary rights of third parties, we
cannot assure you that infringement or invalidity claims (or claims for
indemnification resulting from infringement claims) will not be asserted or
prosecuted against us or that any such assertions or prosecutions will not
materially adversely affect our business, financial condition and results of
operations. Regardless of the validity of such claims, defending against such
claims could result in significant costs and diversion of our resources, which
could have a material adverse effect on our business, financial condition and
results of operations. In addition, the assertion of such infringement claims
could result in injunctions preventing us from distributing certain products,
which could have a material adverse effect on our business, financial condition
and results of operations. If any claims or actions are asserted against us, we
may seek to obtain a license to such intellectual property rights. We cannot
assure you, however, that such a license would be available on reasonable terms
or at all.

     Product Errors.  Highly complex software products, such as ours, often
contain undetected errors or failures when first introduced or as new versions
are released. Testing of the our products is particularly challenging because it
is difficult to simulate the wide variety of computing environments in which our
customers may deploy these products. Despite extensive testing, we from time to
time have discovered defects or errors in our products. Accordingly, we cannot
assure you that such defects, errors or difficulties will not cause delays in
product introductions and shipments, result in increased costs and diversion of
development resources, require design modifications or decrease market
acceptance or customer satisfaction with our products. In addition, we cannot
assure you that, despite testing by us and by current and potential customers,
errors will not be found after commencement of commercial shipments, resulting
in loss of or delay in market acceptance, which could have a material adverse
effect upon our business, financial condition and results of operations.

                                       -9-
<PAGE>   11

               SPECIAL NOTE REGARDING FORWARD-LOOKING INFORMATION

     This prospectus contains or incorporates forward-looking statements within
the meaning of Section 27A of the Securities Act of 1933, as amended (the
"Securities Act"), and Section 21E of the Securities Exchange Act of 1934, as
amended. You can identify these forward-looking statements by our use of the
words "believes," "anticipates," "plans," "expects," "may," "will," "would,"
"intends," "estimates" and similar expressions, whether in the negative or
affirmative. We cannot guarantee that we actually will achieve these plans,
intentions or expectations. Actual results or events could differ materially
from the plans, intentions and expectations disclosed in the forward-looking
statements we make. We have included important factors in the cautionary
statements below (particularly under the heading "Risk Factors") that we believe
could cause our actual results to differ materially from the forward-looking
statements that we make. The forward-looking statements do not reflect the
potential impact of any future acquisitions, mergers or dispositions. We do not
assume any obligation to update any forward-looking statement we make.

                                USE OF PROCEEDS

     We will not receive any proceeds from the sale of shares by the selling
stockholders.

     We will bear all costs (excluding any underwriting discounts and
commissions and expenses incurred by the selling stockholders for brokerage,
accounting, tax or legal services or any other expenses incurred by the selling
stockholders in disposing of the shares), fees and expenses incurred in
effecting the registration of the shares covered by this prospectus, including,
without limitation, all registration and filing fees, Nasdaq listing fees, fees
and expenses of our counsel, fees and expenses of our accountants, and blue sky
fees and expenses.

                                      -10-
<PAGE>   12

                              SELLING STOCKHOLDERS

     The selling stockholders are former stockholders of PowerCenter Systems,
Inc., MSI Solutions, Inc., and MSI Integrated Services, Inc., which we recently
acquired, and Eclipsys stockholders who are parties to the Second Amended and
Restated Registration Rights Agreement, as amended. The following table sets
forth, to our knowledge, information about the selling stockholders as of
November 30, 1999.

     Beneficial ownership is determined in accordance with the rules of the SEC,
and includes voting or investment power with respect to shares. Shares of voting
common stock issuable under stock options that are exercisable within 60 days
after November 30, 1999, are deemed outstanding for computing the percentage
ownership of the person holding the options but are not deemed outstanding for
computing the percentage ownership of any other person. Unless otherwise
indicated below, to our knowledge, all persons named in the table have sole
voting and investment power with respect to their shares of common stock, except
to the extent authority is shared by spouses under applicable law. The inclusion
of any shares in this table does not constitute an admission of beneficial
ownership for the person named below.

<TABLE>
<CAPTION>
                                            SHARES OF VOTING                           SHARES OF VOTING
                                              COMMON STOCK                               COMMON STOCK
                                           BENEFICIALLY OWNED     NUMBER OF SHARES    BENEFICIALLY OWNED
                                           BEFORE OFFERING(1)        OF VOTING       AFTER OFFERING(1)(2)
                                         ----------------------     COMMON STOCK     ---------------------
      NAME OF SELLING STOCKHOLDER         NUMBER     PERCENTAGE    OFFERED HEREBY    NUMBER    PERCENTAGE
      ---------------------------        ---------   ----------   ----------------   -------   -----------
<S>                                      <C>         <C>          <C>                <C>       <C>
Former Stockholders of PowerCenter
Systems, Inc.:
  Paul Michael Breedlove
  805 West 61st Street
  Kansas City, MO 64113-1310...........      2,015        *               2,015       --         --
  Harold Cohan
  P.O. Box 351
  Old Westbury, NY 11568...............     16,484        *              16,484       --         --
  Lori Cohan
  60 Colby Drive
  Dix Hills, NY 11746..................        250        *                 250       --         --
  Seth Cohan
  60 Colby Drive
  Dix Hills, NY 11746..................        250        *                 250       --         --
  Philip S. Ross
  15 Colgate Road
  Great Neck, NY 11023.................        250        *                 250       --         --
  Sharon Ross
  15 Colgate Road
  Great Beck, NY 11023.................        250        *                 250       --         --
  Cathryn Duncan
  7 Potter Court
  Smithtown, NY 11787-1008.............     90,922        *              90,922       --         --
  Matthew Ehrlich(3)
  297 Harvard Avenue
  Rockville Centre, NY 11570-1920......    251,773        *             251,773       --         --
  Paul Ehrlich(3)
  6 Edison Drive
  Huntington Station, NY 11746-4202....    251,773        *             251,773       --         --
</TABLE>

                                      -11-
<PAGE>   13

<TABLE>
<CAPTION>
                                            SHARES OF VOTING                           SHARES OF VOTING
                                              COMMON STOCK                               COMMON STOCK
                                           BENEFICIALLY OWNED     NUMBER OF SHARES    BENEFICIALLY OWNED
                                           BEFORE OFFERING(1)        OF VOTING       AFTER OFFERING(1)(2)
                                         ----------------------     COMMON STOCK     ---------------------
      NAME OF SELLING STOCKHOLDER         NUMBER     PERCENTAGE    OFFERED HEREBY    NUMBER    PERCENTAGE
      ---------------------------        ---------   ----------   ----------------   -------   -----------
<S>                                      <C>         <C>          <C>                <C>       <C>
Euclid Partners IV, L.P.
Attn.: A Bliss McCrum
45 Rockefeller Plaza, Suite 907
New York, NY 10111.....................    443,792      1.3%            443,792       --         --
  Glenn Goldfarb
  R.R. 2, Box 587
  Sharon Springs, NY 13459-9412........     34,970        *              34,970       --         --
  Erik Krag(3)
  730 Toddson Drive
  Greencastle, IN 46135-9227...........      1,810        *               1,810       --         --
  Danielle Larocca(3)
  30 Clearwater Avenue
  Nassau Shores
  Massapequa, NY 11758-8240............        227        *                 227       --         --
  Robert Strangio(3)
  97 Shepherd Street
  Rockville Centre, NY 11570-2249......      3,619        *               3,619       --         --
  Peter Tong
  685 Spring Street, 210
  Friday Harbor, WA 98250-8058.........      5,411        *               5,411       --         --

Former Stockholders of MSI Solutions,
  Inc. and MSI Integrated Solutions:
  1997 Feldman Family Trust
  c/o Robert J. Feldman
  1909 Thomas Bishop Lane
  Virginia Beach, VA 23454.............    367,531      1.1%            367,531       --         --
  Anna L. Bean(3)
  18 Peppertree Court
  Marietta, GA 30068...................  1,225,103      3.5%          1,225,103       --         --
  Michael R. Cote(3)
  1650 Lazy River Lane
  Dunwoody, GA 30350...................    113,934        *             113,934       --         --
  Robert J. Feldman(3)
  1909 Thomas Bishop Lane
  Virginia Beach, VA 23454.............    551,296      1.6%            551,296       --         --

Stockholders Party to the Registration
  Rights Agreement:
  Motorola, Inc.
  Attn: Robert Kell
  1301 East Algonquin Road
  Schaumberg, IL 60196-4041............  1,000,000      2.9%          1,000,000       --         --
</TABLE>

                                      -12-
<PAGE>   14


<TABLE>
<CAPTION>
                                            SHARES OF VOTING                           SHARES OF VOTING
                                              COMMON STOCK                               COMMON STOCK
                                           BENEFICIALLY OWNED     NUMBER OF SHARES    BENEFICIALLY OWNED
                                           BEFORE OFFERING(1)        OF VOTING       AFTER OFFERING(1)(2)
                                         ----------------------     COMMON STOCK     ---------------------
      NAME OF SELLING STOCKHOLDER         NUMBER     PERCENTAGE    OFFERED HEREBY    NUMBER    PERCENTAGE
      ---------------------------        ---------   ----------   ----------------   -------   -----------
<S>                                      <C>         <C>          <C>                <C>       <C>
Warburg, Pincus Ventures, L.P.(4)
Attn.: Patrick T. Hackett
466 Lexington Avenue
New York, NY 10017-3140................  3,215,625      9.2%          3,215,625       --         --
Other Warburg Selling Stockholders(4):
  Warburg, Pincus & Co.................    516,225      1.5%            516,225       --         --
  Springbrook, G.P., a Delaware
     Partnership.......................    280,918        *             280,918       --         --
  Northern Trust Company, as Trustee of
     the Lucent Technologies, Inc.
     Master Pension Trust..............    216,283        *             216,283       --         --
  New York State Common Retirement
     Fund..............................    176,456        *             176,456       --         --
  California State Teachers' Retirement
     System............................    155,281        *             155,281       --         --
  Warburg, Pincus Partners LLC.........    150,000        *             150,000       --         --
  Marinecrew & Co., by State Street
     Bank and Trust Co., as Trustee....    141,165        *             141,165       --         --
  Public Employees' Retirement
     Association of Colorado...........    141,165        *             141,165       --         --
  Chase Manhattan Bank, as trustee for
     IBM Retirement Plan Trust.........    141,165        *             141,165       --         --
  Washington State Investment Board....    141,165        *             141,165       --         --
  Leeway & Co..........................    136,627        *             136,627       --         --
  Northwest Airlines Inc. Master
     Trust.............................     84,699        *              84,699       --         --
  Lockheed Martin Corporation Master
     Retirement Trust..................     70,582        *              70,582       --         --
  Michigan Public School Employees,
     State Employees, State Police and
     Judges Retirement Systems.........     70,582        *              70,582       --         --
  Minnesota State Board of
     Investments.......................     70,582        *              70,582       --         --
  Philip Morris Master Retirement
     Fund..............................     70,582        *              70,582       --         --
  SBC Master Pension Trust.............     70,582        *              70,582       --         --
  Bristol-Myers Squibb Company Defined
     Benefit Master Trust..............     56,466        *              56,466       --         --
  Bankers Trust Company, as Directed
     Trustee of the Southern Company
     System Master Retirement Trust....     56,466        *              56,466       --         --
  Mellon Bank N.A. as Trustee for the
     Kresge Foundation.................     49,408        *              49,408       --         --
  International Bank for Reconstruction
     and Development on behalf of its
     Staff Retirement Plan.............     43,761        *              43,761       --         --
</TABLE>


                                      -13-
<PAGE>   15


<TABLE>
<CAPTION>
                                            SHARES OF VOTING                           SHARES OF VOTING
                                              COMMON STOCK                               COMMON STOCK
                                           BENEFICIALLY OWNED     NUMBER OF SHARES    BENEFICIALLY OWNED
                                           BEFORE OFFERING(1)        OF VOTING       AFTER OFFERING(1)(2)
                                         ----------------------     COMMON STOCK     ---------------------
      NAME OF SELLING STOCKHOLDER         NUMBER     PERCENTAGE    OFFERED HEREBY    NUMBER    PERCENTAGE
      ---------------------------        ---------   ----------   ----------------   -------   -----------
<S>                                      <C>         <C>          <C>                <C>       <C>
Boston Safe Deposit and Trust Co., as
Trustee for the Retirement Income Plan
Trust of the Minnesota Mining and
Manufacturing Co. .....................     42,349        *              42,349       --         --
  Assur Investments LLC................     35,291        *              35,291       --         --
  State Street Bank & Trust Co as
     Trustee for the ConAgra Master
     Trust.............................     35,291        *              35,291       --         --
  General Reinsurance Corp. ...........     35,291        *              35,291       --         --
  GTE Service Corporation Plan for
     Employees Pension.................     35,291        *              35,291       --         --
  Howard Hughes Medical Institute......     35,291        *              35,291       --         --
  Suprapart AG.........................     33,880        *              33,880       --         --
  Illinois State Board of Investment...     28,233        *              28,233       --         --
  International Monetary Fund Staff
     Retirement Plan...................     28,233        *              28,233       --         --
  Lateen & Co. ........................     28,233        *              28,233       --         --
  Other selling stockholders (48
     persons or entities each holding
     less than 25,000 shares, or less
     than 0.1% each)...................    307,738        *             307,738       --         --
</TABLE>


- ---------------
 *  Less than one percent of the total number of shares of voting common stock
    outstanding.

(1) Of the total shares of voting common stock listed as owned by the selling
    stockholders, a total of 106,302 shares are held in escrow accounts to
    secure indemnification obligations to Eclipsys Corporation of the former
    stockholders of PowerCenter Systems, Inc. It is expected that all of these
    shares (less any shares that may be distributed from the escrow account to
    Eclipsys Corporation in satisfaction of indemnification claims) will be
    released from escrow and distributed to the PowerCenter Systems, Inc.
    stockholders on February 17, 2000. The number of shares indicated as owned
    by each former stockholders of PowerCenter Systems, Inc. includes those
    shares (representing 10% of the number of shares listed as beneficially
    owned by each selling stockholder) which such selling stockholder is
    entitled to receive upon distribution of these shares from the escrow
    account.

(2) We do not know when or in what amounts a selling stockholder may offer
    shares for sale. The selling stockholders may decide not to sell any or all
    of the shares offered by this prospectus. Because the selling stockholders
    may offer all or some of the shares pursuant to this offering, and because
    there are currently no agreements, arrangements or understandings with
    respect to the sale of any of the shares that will be held by the selling
    stockholders after completion of the offering, we cannot estimate the number
    of the shares that will be held by the selling stockholders after completion
    of the offering. However, for purposes of this table, we have assumed that,
    after completion of the offering, none of the shares covered by this
    prospectus will be held by the selling stockholders.

(3) Employees or former employees of Eclipsys Corporation, PowerCenter Systems,
    Inc, MSI Integrated Services, Inc. and/or MSI Solutions, Inc.


(4) Warburg, Pincus Ventures, L.P. currently owns all of the 3,215,625 shares of
    voting common stock shown as being held by it. From time to time, Warburg,
    Pincus Ventures, L.P. may decide to distribute a portion or all of its
    shares to the selling stockholders identified in the table as "Other Warburg
    Selling Stockholders" in connection with a partnership distribution. The
    number of shares shown opposite the name of each Other Warburg Selling
    Stockholder is the maximum number of


                                      -14-
<PAGE>   16


    shares that might be distributed to it based on its ownership interest in
    Warburg, Pincus Ventures, L.P. and the maximum number that may be offered by
    it under this prospectus. In no event will the maximum number of shares
    distributed to or offered by the Other Warburg Selling Stockholders as a
    group exceed 3,215,625. The address of each Other Warburg Selling
    Stockholder is c/o Warburg, Pincus Ventures, L.P., 466 Lexington Avenue, New
    York, New York 10017.


     None of the selling stockholders has held any position or office with, or
has otherwise had a material relationship with, Eclipsys Corporation or any of
its subsidiaries within the past three years, except that Patrick T. Hackett, a
partner of the general partner of Warburg, Pincus Ventures, L.P., is a director
of Eclipsys Corporation, Robert Kell, a corporate vice president of Motorola,
Inc., is a director of Eclipsys Corporation and the other selling stockholders
indicated have been employed by Eclipsys Corporation, PowerCenter Systems, Inc,
MSI Integrated Services, Inc. and/or MSI Solutions, Inc. In connection with the
acquisition of MSI Solutions, Inc. and MSI Integrated Services, Inc., Eclipsys
Corporation entered into employment agreements with Anna Bean and Robert J.
Feldman, each formerly of MSI Solutions, Inc. and MSI Integrated Services, Inc.,
under which each will perform certain services for Eclipsys Corporation through
June 17, 2002.

                              PLAN OF DISTRIBUTION

     The shares covered hereby may be offered and sold from time to time by the
selling stockholders. The term "selling stockholders" includes donees, pledgees,
transferees or other successors in interest selling shares received after the
date of this prospectus from a selling stockholder as a gift, pledge,
partnership distribution or other non-sale related transfer. The selling
stockholders will act independently of Eclipsys Corporation in making decisions
with respect to the timing, manner and size of each sale. Such sales may be made
in the over-the-counter market or otherwise, at prices and under terms then
prevailing or at prices related to the then current market price or in
negotiated transactions, including pursuant to one or more of the following
methods:

          1. purchases by a broker-dealer as principal and resale by such
     broker-dealer for its own account pursuant to this prospectus;

          2. ordinary brokerage transactions and transactions in which the
     broker solicits purchasers;

          3. block trades in which the broker-dealer so engaged will attempt to
     sell the shares as agent but may position and resell a portion of the block
     as principal to facilitate the transaction;

          4. an over-the-counter distribution in accordance with the rules of
     the Nasdaq National Market;

          5. in privately negotiated transactions; and

          6. in options transactions.


     To the extent required, this prospectus may be amended and supplemented
from time to time to describe a specific plan of distribution. In connection
with distributions of the shares or otherwise, the selling stockholders may
enter into hedging transactions with broker-dealers or other financial
institutions. In connection with such transactions, broker-dealers or other
financial institutions may engage in short sales of the voting common stock in
the course of hedging the positions they assume with selling stockholders. The
selling stockholders may also sell the voting common stock short and redeliver
the shares to close out such short positions. The selling stockholders may also
enter into option or other transactions with broker-dealers or other financial
institutions which require the delivery to such broker-dealer or other financial
institution of shares offered by this prospectus, which shares such
broker-dealer or other financial institution may resell pursuant to this
prospectus (as supplemented or amended to reflect such transaction). The selling
stockholders may also pledge shares to a broker-dealer or other financial
institution, and, upon a default, such broker-dealer or other financial
institution, may effect sales of the pledged shares pursuant to this prospectus
(as supplemented or amended to reflect such transaction). In addition, any
shares that qualify for sale pursuant to Rule 144 and, if applicable, Rule 145
may be sold under Rule 144 and Rule 145 rather than pursuant to this prospectus.

                                      -15-
<PAGE>   17

     In effecting sales, broker-dealers or agents engaged by the selling
stockholders may arrange for other broker-dealers to participate. Broker-dealers
or agents may receive commissions, discounts or concessions from the selling
stockholders in amounts to be negotiated immediately prior to the sale.

     In offering the shares covered hereby, the selling stockholders and any
broker-dealers and any other participating broker-dealers who execute sales for
the selling stockholders may be deemed to be "underwriters" within the meaning
of the Securities Act in connection with such sales. Any profits realized by the
selling stockholders and the compensation of any broker-dealer may be deemed to
be underwriting discounts and commissions.

     In order to comply with the securities laws of certain states, if
applicable, the shares must be sold in such jurisdictions only through
registered or licensed brokers or dealers. In addition, in certain states the
shares may not be sold unless they have been registered or qualified for sale in
the applicable state or an exemption from the registration or qualification
requirement is available and is complied with.

     We have advised the selling stockholders that the anti-manipulation rules
of Regulation M under the Exchange Act may apply to sales of shares in the
market and to the activities of the selling stockholders and their affiliates.
In addition, we will make copies of this prospectus available to the selling
stockholders for the purpose of satisfying the prospectus delivery requirements
of the Securities Act. The selling stockholders may indemnify any broker-dealer
that participates in transactions involving the sale of the shares against
certain liabilities, including liabilities arising under the Securities Act.

     At the time a particular offer of shares is made, if required, a prospectus
supplement will be distributed that will set forth the number of shares being
offered and the terms of the offering, including the name of any underwriter,
dealer or agent, the purchase price paid by any underwriter, any discount,
commission and other item constituting compensation, any discount, commission or
concession allowed or reallowed or paid to any dealer, and the proposed selling
price to the public.

     We have agreed to indemnify some of the selling stockholders against some
liabilities, including liabilities under the Securities Act.

     We have agreed with the selling stockholders to keep the Registration
Statement of which this prospectus constitutes a part effective until the
earlier of (i) such time as all of the shares covered by this prospectus have
been disposed of pursuant to and in accordance with the Registration Statement
or (ii) June 17, 2001.

                                 LEGAL MATTERS

     The validity of the shares offered by this prospectus has been passed upon
by Hale and Dorr LLP.

                                    EXPERTS

     The audited financial statements incorporated in this Prospectus by
reference to the Annual Report on Form 10-K of Eclipsys Corporation for the year
ended December 31, 1998 (which have not been restated to give effect to the
pooling of interests business combinations with PowerCenter Systems, Inc., MSI
Solutions, Inc. and MSI Integrated Services, Inc.) have been so incorporated in
reliance on the report of PricewaterhouseCoopers LLP, independent accountants,
given on the authority of said firm as experts in auditing and accounting.

     The audited financial statements incorporated in this Prospectus by
reference to the Eclipsys Corporation Current Report on Form 8-K dated December
7, 1999, except as they relate to the financial statements of PowerCenter
Systems, Inc. for the year ended December 31, 1996 (not presented therein), have
been audited by PricewaterhouseCoopers LLP, independent accountants, and,
insofar as they relate to the financial statements of PowerCenter Systems, Inc.
for the year ended December 31, 1996 by Ernst & Young LLP, independent
accountants, whose reports are incorporated herein. Such financial statements of

                                      -16-
<PAGE>   18

Eclipsys Corporation have been so incorporated in reliance on the reports of
such independent accountants given on the authority of such firms as experts in
auditing and accounting.

     The audited financial statements of ALLTEL Healthcare Information Services,
Inc. as of January 23, 1997, December 31, 1996 and 1995 and for the period from
January 1, 1997 through January 23, 1997 and each of the two years in the period
ended December 31, 1996 incorporated in this Prospectus by reference to Eclipsys
Corporation's Form 8-K dated December 7, 1999 have been so incorporated in
reliance on the report of PricewaterhouseCoopers LLP, independent accountants,
given on the authority of said firm as experts in auditing and accounting.

                         WHERE TO FIND MORE INFORMATION

     We file annual, quarterly, and current reports, proxy statements, and other
documents with the Securities and Exchange Commission. You may read and copy any
document we file at the SEC's public reference room at Judiciary Plaza Building,
450 Fifth Street, N.W., Room 1024, Washington, D.C. 20549. You should call
1-800-SEC-0330 for more information on the public reference room. Our SEC
filings are also available to you on the SEC's Internet site at
http://www.sec.gov. Our voting common stock is quoted on Nasdaq.

     This prospectus is part of a registration statement that we filed with the
SEC. The registration statement contains more information than this prospectus
regarding Eclipsys Corporation and the voting common stock, including certain
exhibits and schedules. You can obtain a copy of the registration statement from
the SEC at the address listed above or from its internet site.

                INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE

     The SEC allows us to "incorporate" into this prospectus information we file
with the SEC in other documents. This means that we can disclose important
information to you by referring to other documents that contain that
information. The information incorporated by reference is considered to be part
of this prospectus, and information that we file with the SEC in the future and
incorporate by reference will automatically update and may supersede the
information contained in this prospectus. We incorporate by reference the
documents listed below and any future filings we make with the SEC under
Sections 13(a), 13(c), 14 or 15(d) of the Securities Exchange Act of 1934, as
amended, prior to the sale of all the shares covered by this prospectus.

     The following documents that we have filed with the SEC are incorporated
herein by reference:

          (i) Our Annual Report on Form 10-K for the year ended December 31,
              1998;

         (ii) Our Quarterly Report on Form 10-Q for the quarter ended March 31,
              1999;

         (iii) Our Quarterly Report on Form 10-Q for the quarter ended June 30,
               1999;

         (iv) Our Current Report on Form 8-K, filed with the SEC on August 30,
              1999;

          (v) Our Quarterly Report on Form 10-Q for the quarter ended September
              30, 1999;

         (vi) Our Current Report on Form 8-K, filed with the SEC on December 7,
              1999;

         (vii) All of our filings pursuant to the Exchange Act after the date of
               filing the initial registration statement and prior to
               effectiveness of the registration statement; and

        (viii) The description of our voting common stock contained in our
               Registration Statement on Form 8-A, including any amendments or
               reports filed for the purpose of updating such description.

                                      -17-
<PAGE>   19

     You may request a copy of these documents, at no cost, by writing to:

                       Eclipsys Corporation
                       777 East Atlantic Avenue, Suite 200
                       Delray Beach, Florida 33483
                       Attention: Robert J. Colletti
                       Telephone: (561) 243-1442

                                      -18-
<PAGE>   20

                                    PART II

                     INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14.  OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

     The following table sets forth the various expenses to be incurred in
connection with the sale and distribution of the securities being registered
hereby, all of which will be borne by Eclipsys Corporation (except any
underwriting discounts and commissions and expenses incurred by the selling
stockholders for brokerage, accounting, tax or legal services or any other
expenses incurred by the selling stockholders in disposing of the shares). All
amounts shown are estimates except the Securities and Exchange Commission
registration fee.

<TABLE>
<S>                                                           <C>
Filing Fee -- Securities and Exchange Commission............  $ 33,515
Legal fees and expenses.....................................  $ 20,000
Accounting fees and expenses................................  $ 35,000
Miscellaneous expenses......................................  $ 20,000
                                                              --------
          Total Expenses....................................  $108,515
                                                              ========
</TABLE>

ITEM 15.  INDEMNIFICATION OF DIRECTORS AND OFFICERS.

     Section 102 of the Delaware General Corporation Law allows a corporation to
eliminate the personal liability of directors of a corporation to the
corporation or its stockholders for monetary damages for a breach of fiduciary
duty as a director, except where the director breached his duty of loyalty,
failed to act in good faith, engaged in intentional misconduct or knowingly
violated a law, authorized the payment of a dividend or approved a stock
repurchase in violation of Delaware corporate law or obtained an improper
personal benefit. Eclipsys Corporation has included such a provision in its
Certificate of Incorporation.

     Section 145 of the General Corporation Law of Delaware provides that a
corporation has the power to indemnify a director, officer, employee or agent of
the corporation and certain other persons serving at the request of the
corporation in related capacities against amounts paid and expenses incurred in
connection with an action or proceeding to which he is or is threatened to be
made a party by reason of such position, if such person shall have acted in good
faith and in a manner he reasonably believed to be in or not opposed to the best
interests of the corporation, and, in any criminal proceeding, if such person
had no reasonable cause to believe his conduct was unlawful; provided that, in
the case of actions brought by or in the right of the corporation, no
indemnification shall be made with respect to any matter as to which such person
shall have been adjudged to be liable to the corporation unless and only to the
extent that the adjudicating court determines that such indemnification is
proper under the circumstances. The Certificate of Incorporation contains
provisions to indemnify the Company's directors and officers to the fullest
extent permitted by the General Corporation Law of Delaware.

     Eclipsys Corporation has purchased directors' and officers' liability
insurance which would indemnify its directors and officers against damages
arising out of certain kinds of claims which might be made against them based on
their negligent acts or omissions while acting in their capacity as such.

ITEM 16.  EXHIBITS


<TABLE>
<CAPTION>
EXHIBIT
NUMBER                            DESCRIPTION
- -------                           -----------
<C>       <S>
  4.1*    Third Amended and Restated Certificate of Incorporation of
          the Registrant.
  4.2*    By-laws of the Registrant.
  5.1**   Opinion of Hale and Dorr LLP.
 23.1     Consent of PricewaterhouseCoopers LLP.
</TABLE>


                                      II-1
<PAGE>   21


<TABLE>
<CAPTION>
EXHIBIT
NUMBER                            DESCRIPTION
- -------                           -----------
<C>       <S>
 23.2     Consent of PricewaterhouseCoopers LLP.
 23.3     Consent of Ernst & Young LLP
 23.4**   Consent of Hale and Dorr LLP, included in Exhibit 5.1 filed
          herewith.
 24.1**   Power of Attorney.
</TABLE>


- ---------------
 * Incorporated by reference from Registration Statement on Form S-1, File
   Number 333-50781.


** Previously filed.


ITEM 17.  UNDERTAKINGS.

     The undersigned Registrant hereby undertakes:

          (1) To file, during any period in which offers or sales are being
     made, a post-effective amendment to this Registration Statement:

             (i) To include any prospectus required by Section 10(a)(3) of the
        Securities Act of 1933, as amended (the "Securities Act");

             (ii) To reflect in the prospectus any facts or events arising after
        the effective date of this Registration Statement (or the most recent
        post-effective amendment thereof) which, individually or in the
        aggregate, represent a fundamental change in the information set forth
        in this Registration Statement. Notwithstanding the foregoing, any
        increase or decrease in the volume of securities offered (if the total
        dollar value of securities offered would not exceed that which was
        registered) and any deviation from the low or high end of the estimated
        maximum offering range may be reflected in the form of prospectus filed
        with the Commission pursuant to Rule 424(b) if, in the aggregate, the
        changes in volume and price represent no more than 20 percent change in
        the maximum aggregate offering price set forth in the "Calculation of
        Registration Fee" table in the effective Registration Statement; and

             (iii) To include any material information with respect to the plan
        of distribution not previously disclosed in this Registration Statement
        or any material change to such information in this Registration
        Statement;

        provided, however, that paragraphs (1)(i) and (1)(ii) do not apply if
        the information required to be included is a post-effective amendment by
        those paragraphs is contained in periodic reports filed by the Company
        pursuant to Section 13 or Section 15(d) of the Securities Exchange Act
        of 1934, as amended (the "Exchange Act"), that are incorporated by
        reference in this Registration Statement.

          (2) That, for the purposes of determining any liability under the
     Securities Act, each post-effective amendment that contains a form of
     prospectus shall be deemed to be a new registration statement relating to
     the securities offered therein, and the offering of such securities at the
     time shall be deemed to be the initial bona fide offering thereof.

          (3) To remove from registration by means of a post-effective amendment
     any of the securities being registered which remain unsold at the
     termination of the offering.

     The Registrant hereby undertakes that, for purposes of determining any
liability under the Securities Act, each filing of the Registrant's annual
report pursuant to Section 13(a) or 15(d) of the Exchange Act (and, where
applicable, each filing of an employee benefit plan's annual report pursuant to
Section 15(d) of the Exchange Act) that is incorporated by reference in this
Registration Statement shall be deemed to be a new registration statement
relating to the securities offered therein and the offering of such securities
at the time shall be deemed to be the initial bona fide offering thereof.

                                      II-2
<PAGE>   22

     Insofar as indemnification for liabilities arising under the Securities Act
may be permitted to directors, officers and controlling persons of the
Registrant pursuant to the indemnification provisions described herein, or
otherwise, the Registrant has been advised that in the opinion of the Securities
and Exchange Commission such indemnification is against public policy as
expressed in the Securities Act and is, therefore, unenforceable. In the event
that a claim for indemnification against such liabilities (other than the
payment by the Registrant of expenses incurred or paid by a director, officer or
controlling person of the Registrant in the successful defense of any action,
suit or proceeding) is asserted by such director, officer or controlling person
in connection with the securities being registered, the Registrant will, unless
in the opinion of its counsel the matter has been settled by controlling
precedent, submit to a court of appropriate jurisdiction the question whether
such indemnification by it is against public policy as expressed in the
Securities Act and will be governed by the final adjudication of such issue.

                                      II-3
<PAGE>   23

                                   SIGNATURES


     Pursuant to the requirements of the Securities Act of 1933, as amended, the
Registrant certifies that it has reasonable grounds to believe that it meets all
of the requirements for filing on Form S-3 and has duly caused this Amendment
No. 1 to the Registration Statement to be signed on its behalf by the
undersigned, thereunto duly authorized, in Delray Beach, Florida, on December
21, 1999.


                                          Eclipsys Corporation

                                          By: /s/ HARVEY J. WILSON
                                            ------------------------------------
                                              Harvey J. Wilson

                                              Chief Executive Officer


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


<TABLE>
<CAPTION>
            SIGNATURE                               TITLE                         DATE
            ---------                               -----                         ----
<S>                                   <C>                                   <C>
/s/ HARVEY J. WILSON                  President, Chief Executive Officer    December 21, 1999
- ----------------------------------    and Director (Principal Executive
Harvey J. Wilson                      Officer)

/s/ ROBERT J. VANARIA                 Chief Financial Officer (Principal    December 21, 1999
- ----------------------------------    Financial and Accounting Officer)
Robert J. Vanaria

*                                     Director                              December 21, 1999
- ----------------------------------
J. Robert Kell

*                                     Director                              December 21, 1999
- ----------------------------------
William E. Ford

*                                     Director                              December 21, 1999
- ----------------------------------
Steven A. Denning

*                                     Director                              December 21, 1999
- ----------------------------------
Jay B. Pieper

*                                     Director                              December 21, 1999
- ----------------------------------
G. Fred DiBona

*                                     Director                              December 21, 1999
- ----------------------------------
Eugene V. Fife

*                                     Director                              December 21, 1999
- ----------------------------------
Patrick T. Hackett

    * By: /s/ HARVEY J. WILSON
- ----------------------------------
         Harvey J. Wilson
         Attorney-in-fact
</TABLE>


                                      II-4
<PAGE>   24

                                 EXHIBIT INDEX


<TABLE>
<CAPTION>
EXHIBIT
NUMBER                            DESCRIPTION
- -------                           -----------
<C>       <S>
  4.1*    Third Amended and Restated Certificate of Incorporation.
  4.2*    By-laws of the Registrant.
  5.1**   Opinion of Hale and Dorr LLP.
 23.1     Consent of PricewaterhouseCoopers, LLP.
 23.2     Consent of PricewaterhouseCoopers, LLP.
 23.3     Consent of Ernst & Young LLP.
 23.4**   Consent of Hale and Dorr LLP, included in Exhibit 5.1 filed
          herewith.
 24.1**   Power of Attorney.
</TABLE>


- ---------------
 * Incorporated by reference to Registration Statement on Form S-1, File Number
   333-50781.


** Previously filed.


<PAGE>   1

                                                                    EXHIBIT 23.1

                       CONSENT ON INDEPENDENT ACCOUNTANTS

     We hereby consent to the incorporation by reference in this Amendment No. 1
to the Registration Statement on Form S-3 (No. 333-92251) of our report dated
June 27, 1997 relating to the financial statements of Alltel Healthcare
Information Services, Inc. which appears in the Current Report on Form 8-K dated
December 7, 1999. We also consent to the reference to us under the heading
"Experts" in such Registration Statement.

                                          /s/ PricewaterhouseCoopers LLP

Atlanta, Georgia
December 21, 1999

<PAGE>   1

                                                                    EXHIBIT 23.2

                       CONSENT OF INDEPENDENT ACCOUNTANTS

     We hereby consent to the incorporation by reference in this Amendment No. 1
to the Registration Statement on Form S-3 (No. 333-92251) of our report dated
February 19, 1999 related to the financial statements (which financial
statements have not been restated to give effect to the pooling of interests
business combinations with PowerCenter Systems, Inc., MSI Solutions, Inc. and
MSI Integrated Services, Inc.), which appears in Eclipsys Corporation's Annual
Report on Form 10-K for the year ended December 31, 1998. We also consent to the
incorporation by reference of our report dated February 19, 1999, except as to
the acquisition of Intellus Corporation and Med Data Systems, Inc. which is as
of March 31, 1999, the pooling of interests with MSI Solutions, Inc. and MSI
Integrated Services, Inc. which is as of June 17, 1999, the sale of Med Data
Systems, Inc. which is as of July 1, 1999, and the investment in HEALTHvision,
Inc. which is as July 16, 1999, which are described in Note 15, relating to the
financial statements, which appears in the Current Report on Form 8-K dated
December 7, 1999. We also consent to the references to us under the heading
"Experts" in such Registration Statement.

                                          /s/ PricewaterhouseCoopers LLP

Atlanta, Georgia
December 21, 1999

<PAGE>   1

                                                                    EXHIBIT 23.3

                        CONSENT OF INDEPENDENT AUDITORS

     We consent to the reference to our firm under the caption "Experts" and to
the use of our report dated March 20, 1998, except as to Note 9(a), as to which
the date is July 30, 1998, and Note 9(b), as to which the date is February 5,
1999, with respect to the financial statements of PowerCenter Systems, Inc. (not
presented herein) in this Amendment No. 1 to the Registration Statement (Form
S-3, No. 333-92251) and related Prospectus of Eclipsys Corporation for the
registration of 7,577,285 shares of its common stock.

                                                 /s/ ERNST & YOUNG LLP

Melville, New York
December 21, 1999


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