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As filed with the Securities and Exchange Commission on September 13, 2004

Registration No. 333-

SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

FORM S-3
REGISTRATION STATEMENT

Under
THE SECURITIES ACT OF 1933

CLICK COMMERCE, INC.

(Exact name of registrant as specified in its charter)

Delaware		7371		36-4088644
(State or other jurisdiction of incorporation or organization)		(Primary Standard Industrial Classification Code Number)		(I.R.S. Employer Identification No.)

200 East Randolph Drive, 52nd Floor
Chicago, Illinois 60601
(312) 482-9006

(Address, including zip code, and telephone number, including area code, of registrant's principal executive offices)

Justin Dearborn
Click Commerce, Inc.
200 East Randolph Drive, 52nd Floor
Chicago, Illinois 60601
(312) 482-9006

(Name, address, including zip code, and telephone number, including area code, of agent for service)

Copies to
Mark A. Harris
McDermott Will & Emery LLP
227 W. Monroe Street
Chicago, IL 60606
(312) 372-2000

Approximate date of commencement of proposed sale to the public: From time to time after the effective date of this registration statement.

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

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, check the following box. ý

If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) 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. o

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. o

If delivery of the prospectus is expected to be made pursuant to Rule 434, check the following box

CALCULATION OF REGISTRATION FEE

Title of Each Class of Securities to be Registered	Amount to be Registered	Proposed Maximum Offering Price Per Unit(1)	Proposed Maximum Aggregate Offering Price(1)	Amount of Registration Fee


Common Stock	698,398	$4.88	$3,408,182	$431.82

(1): Estimated solely for the purpose of calculating the registration fee in accordance with Rule 457(c) under the Securities Act of 1933, and based on the average of the high and low prices of the common stock on September 3, 2004 as reported on the NASDAQ National Market.

The registrant hereby amends this registration statement on such date or dates as may be necessary to delay its effective date until the registrant 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 this registration statement shall become effective on such date as the Securities and Exchange Commission, acting pursuant to said Section 8(a), may determine.

The information in this preliminary prospectus is not complete and may be changed. These securities may not be sold until the registration statement filed with the Securities and Exchange Commission is effective. This preliminary prospectus is not an offer to sell nor does it seek an offer to buy these securities in any jurisdiction where the offer or sale is not permitted.

Subject to Completion. Dated September 13, 2004.

698,398 Shares

Common Stock

The selling stockholders identified in this prospectus may offer from time to time up to 698,398 shares of common stock of Click Commerce, Inc. We will not receive any of the proceeds from the sale of the shares. We have agreed to pay for the expenses of the offering.

This prospectus describes the general manner in which shares of common stock may be offered and sold by the selling stockholders. If necessary, the specific manner in which shares of common stock may be offered and sold will be described in a supplement to this prospectus.

Our common stock is quoted on the NASDAQ National Market under the symbol "CKCM". The last reported sale price of common stock on September 10, 2004 was $6.10 per share.

See "Risk Factors" beginning on page 3 to read about factors you should consider before buying shares of common stock.

Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or passed upon the adequacy or accuracy of this prospectus. Any representation to the contrary is a criminal offense.

Prospectus dated [ ], 2004.

IMPORTANT NOTICE TO READERS

This prospectus is part of a registration statement that we filed with the Securities and Exchange Commission, using a "shelf" registration process. Under this shelf registration process, the selling stockholders may, from time to time, offer shares of our common stock owned by them. Each time the selling stockholders offer common stock under this prospectus, they will provide a copy of this prospectus and, if applicable, a copy of a prospectus supplement. You should read both this prospectus and, if applicable, any prospectus supplement together with the information incorporated by reference in this prospectus and, if applicable, any supplement hereto. See "Where You Can Find More Information" and "Incorporation of Certain Documents by Reference" for more information.

We have not authorized anyone to provide you with information other than the information contained or incorporated by reference as set forth under "Incorporation of Certain Documents by Reference". The selling stockholders are not making an offer to sell these securities in any jurisdiction where the offer or sale is not permitted. The information contained in this prospectus speaks only as of the date of this prospectus and the information in the documents incorporated or deemed to be incorporated by reference in this prospectus speaks only as of the respective dates those documents were filed with the Securities and Exchange Commission (the "SEC").

TABLE OF CONTENTS

		Page
Click Commerce		1
Risk Factors		3
Forward-Looking Statements		9
Use of Proceeds		9
Dividend Policy		9
Description of Capital Stock		10
Material United States Federal Income Tax Considerations For Non-U.S. Holders		13
Selling Stockholders		16
Plan of Distribution		18
Where You Can Find More Information		20
Incorporation of Certain Documents by Reference		21
Legal Matters		22
Experts		22

CLICK COMMERCE, INC.

Click Commerce provides extranet solutions for channel management, collaborative commerce, and compliance automation. Click solutions are used by enterprises and institutions in the manufacturing, high tech, financial services, retail, healthcare and higher education industries.

Our extranet solutions provide an efficient, electronic way for trading partners to communicate and transact business. Research institutions use a solution that automates compliance reporting for complex research projects and eliminates paper-intensive processes. The Click software solution enables companies to strengthen and broaden their relationships with their partners, as well as their customers, through continuous access to information and the ability to more efficiently process transactions.

Leading corporations such as Microsoft, Delphi, Honda, Citibank, FedEx, Carrier, Samsung, Kawasaki, Logitech, Hitachi, and Tellabs have improved their business relationships with partners and customers using Click Commerce solutions. Six of the top ten National Institute of Health research institutions in North America, including Johns Hopkins, the University of Washington, and the University of Michigan, use the Company's compliance automation software to automate their regulatory compliance processes and manage research project approvals.

Channel Management

Many global companies provide sales, service and after-market support for their goods and services through complex distribution channels. These channels have traditionally been constrained by inefficient, labor intensive, error-prone communication processes delivered via mail, phone and fax. By utilizing the Internet, our software applications permit faster and more accurate transaction processing and communication than these traditional methods. Our software applications can advance the commercial relationships between a company and its distribution channel partners and provide benefits to all participants by improving efficiency, financial performance, customer service and brand loyalty.

Collaborative Commerce

Click Commerce provides e-commerce systems that provide companies of all sizes a scalable suite of products and services to reduce cost and accelerate business processes. Through its recent acquisition of bTrade, Inc., Click Commerce has entered the retail/consumer packaged goods marketplace, and has established itself as a Uniform Code Council-certified Solution Partner. bTrade, a wholly owned subsidiary of Click Commerce, was one of the first companies accepted into the Global Data Synchronization Network (GDSN). It is a preferred data synchronization partner for The Home Depot and a national consumer packaged goods retailer.

Compliance Automation

Hospitals and research institutions face many regulatory and grant compliance requirements that must produce clear, auditable evidence of the compliance processes performed. This evidence has traditionally been documented with manually-prepared paper trails. Click Commerce helps institutions reduced these paper trails by connecting departments through administrative Extranets. Prior paper applications in 3, 5 or even 12-parts have been transformed into electronic intelligent web-based forms that logically lead applicants through a sometimes complex compliance process. Formal review and approval processes are transformed into flexible, configurable sequences of workflow steps. Each workflow can also be enhanced or streamlined within the system to accommodate changes that may occur over time.

We currently market our products and integration services through our direct sales force and our joint marketing relationships to global companies that have large distribution networks, as well as to smaller companies that require scalable and reliable e-commerce solutions.

Our principal executive officers are located at 200 East Randolph Drive, 52nd Floor, Chicago, Illinois 60601, and our telephone number at that address is (312) 482-9006.

We maintain a website at www.clickcommerce.com. Information contained on our website is not part of this prospectus.

In this prospectus, "Click Commerce," the "Company," "we," "us" and "our" refer to Click Commerce, Inc. and its subsidiaries.

RISK FACTORS

You should carefully consider each of the risks described below and all other information contained in this prospectus and incorporated herein by reference before making an investment decision. The following risks, as well as other risks and uncertainties that are not yet identified or that we currently think are immaterial, could materially and adversely affect our business, financial condition and results of operations. In that event, the trading price of our common stock could decline, and you could lose part or all of your investment.

Risks Related to Our Business

We have incurred net losses for the past four fiscal years and we may experience losses in the future, which could cause the market price of our stock to decline.

Although we achieved profitability in the third and fourth quarters of 2003 and the first and second quarters of 2004, we can provide no assurance that we will maintain profitability for the remaining third and fourth quarters of 2004 or for the 2004 calendar year. If we are profitable in 2004, we may not sustain or increase profitability in the future. If we do not maintain profitability levels expected by investors, the market price of our common stock will likely decline.

We are dependent on the success of our suite of applications and related services for our success.

To date, substantially all of our revenues have been attributable to sales of licenses of, and subscriptions to, our suite of e-commerce, channel management and compliance automation applications and related services, consisting of hosting, maintenance, site administration, implementation, integration with a customer's existing back-office computer systems and maintenance and support of our software products. We currently expect our suite of e-commerce, channel management and compliance automation applications and related services to account for a substantial portion of our future revenues. Accordingly, factors adversely affecting the pricing of or demand for these offerings, such as competition, changes in the various compliance regulations and environments or technological change, could have a material adverse effect on our business, financial condition, and operating results. Our future financial performance will depend, in significant part, on the successful development, introduction and customer acceptance of new and enhanced versions of our suite of applications and of new products and services we develop. We can provide no assurance that we will be successful in upgrading and continuing to market our suite of applications or that we will successfully develop new products and services or that any new products and services will achieve market acceptance.

Our business is subject to quarterly fluctuations in operating results, which may negatively impact the price of our common stock.

While our base of recurring maintenance, hosting and subscription revenues provides revenues which are more predictable than sales of software licenses and related implementation services, a significant amount of our revenue is not recurring or accurately predictable in succeeding quarters. Our quarterly operating results may vary significantly from quarter to quarter in the future due to the level of continuing sales of software licenses and related implementation services. We have difficulty predicting the volume and timing of contracts, and short delays in closing contracts or in implementation of products can cause our operating results to fall substantially short of anticipated levels for any particular quarter. Our products have long sales cycles, which makes it difficult to predict the periods in which we will recognize revenue and may cause operating results to vary significantly. As a result of these and other factors, we believe that period-to-period comparisons of our historical results of operations are not necessarily meaningful and are not a good predictor of our future performance. We may not be successful in generating and sustaining recurring revenue streams to offset the above effects.

In addition, we may incur expenses in order to develop products and service offerings ancillary to our existing line of products and services. These expenses may affect our earnings and may result in losses in particular quarterly or annual periods.

For all of these reasons, in some future quarters or years our operating results may be below the expectations of investors, which could cause volatility or a decline in the price of our common stock.

Many of our software products are sold under perpetual software licenses that can be individually significant to a particular quarter and increase the variability of reported revenue.

If we are unable to complete a substantial number of sales contracts when anticipated or experience delays in the process on a project or problems with satisfying contract terms, we may have to defer or not recognize revenue, causing our quarterly results to fluctuate and fall below anticipated levels. For contracts in which revenue is recognized using a percentage-of-completion method, we may not be able to recognize all or a portion of the revenue because milestones are not achieved or the level of hours incurred falls short of expectations. If we are unable to complete one or more substantial anticipated license sales or experience problems with satisfying contract terms required for revenue recognition in a particular quarter, we may not be able to recognize revenue when anticipated. We would nonetheless recognize marketing and other expenses, causing our quarterly results to fluctuate and fall below anticipated levels. This could cause our stock price to decline.

Our business could be materially adversely affected as a result of the risks associated with acquisitions and investments.

As part of our business strategy, we seek to acquire businesses that offer complementary products, services or technologies. These acquisitions, including our acquisitions of Allegis Corporation in March 2003, Webridge, Inc. in April 2004 and bTrade, Inc. in July 2004, are accompanied by the risks commonly encountered in an acquisition of a business, which may include, among other things:

•: the effect of the acquisition on our financial and strategic position and reputation
•: the failure of an acquired business to further our strategies
•: the failure of the acquisition to result in expected benefits, which may include benefits relating to enhanced revenues, technology, human resources, costs savings, operating efficiencies and other synergies
•: the difficulty and cost of integrating the acquired business, including costs and delays in implementing common systems and procedures and costs and delays caused by communication difficulties or geographic distances between Company sites
•: the assumption of liabilities of the acquired business, including litigation-related liabilities
•: the potential impairment of acquired assets
•: the lack of experience in new markets, products or technologies or the initial dependence on unfamiliar supply or distribution partners
•: the diversion of our management's attention from other business concerns
•: the impairment of relationships with customers or suppliers of the acquired business or our customers or suppliers
•: the potential loss of key employees of the acquired company
•: the potential incompatibility of business cultures

These factors could have a material adverse effect on our business, results of operations or financial condition. To the extent that we issue shares of our common stock or other rights to purchase

our common stock in connection with any future acquisition, existing stockholders may experience dilution and our earnings per share may decrease.

In addition to the risks commonly encountered in the acquisition of a business as described above, we may also experience risks relating to the challenges and costs of closing a transaction. Further, the risks described above may be exacerbated as a result of managing multiple acquisitions at the same time.

We also seek to invest in businesses that offer complementary products, services or technologies. These investments are accompanied by risks similar to those encountered in an acquisition of a business.

An economic slowdown, particularly in information technology, may adversely impact our business.

Our business has been adversely impacted by economic slowdowns in the past, particularly the decline in information technology spending. The adverse impacts from an economic slowdown may include longer sales cycles, lower average selling prices and reduced bookings and revenue. An extended economic slowdown could adversely impact our business. We may also be unable to re-adjust selling prices of our software to the levels occurring prior to any economic slowdown.

We license certain software from third parties that is incorporated in our product offerings.

We license software from third parties that is incorporated in certain of our product offerings. The functionality of these product offerings is dependent on those third party licenses. The third party software licenses may not continue to be available to us on acceptable terms. The loss of, or inability to maintain, any of these software licenses could result in shipment delays, reductions in revenue or increased costs to replace such software in our products. This could adversely affect our business, operating results and financial condition.

We may not be able to achieve desired growth in our business if we cannot increase the efficiency of our direct, telesales and indirect sales channels, which could negatively affect our stock price.

Many of our products and services offerings require a sophisticated sales effort targeted at several people within our prospective clients' organizations. We believe that our future success is dependent upon developing more economical sales processes which may include establishing in-house telesales capabilities and strategic relationships with third parties. We cannot be sure that we will be successful in achieving these economies in our direct, telesales or indirect sales staff or in establishing these desired relationships or that these third parties will devote adequate resources or have the technical and other sales capabilities to sell our products.

We face competition and may face increased competition in the future.

The market for software products and services that enable business-to-business e-commerce is intensely competitive, highly fragmented and rapidly changing. There are relatively few barriers to entry in the channel management market. We expect competition to persist and intensify, which could result in our losing market share or lowering our prices.

Some of our competitors have advantages over us.

Some of our existing competitors, as well as potential future competitors, have longer operating histories in markets related to ours, greater name recognition, larger customer bases and significantly greater financial, technical and marketing resources than our Company. These advantages may allow them to respond more quickly and effectively to new or emerging technologies and changes in customer requirements. It may also allow them to engage in more extensive research and development, undertake farther-reaching marketing campaigns, adopt more aggressive pricing policies, implement their products and services more rapidly, and make more attractive offers to potential employees and

other business associates. One or more of these companies could adopt a different business strategy for achieving profitability, which could allow them to charge fees that are lower than ours, in order to attract clients. In addition, current and potential competitors have established or may establish cooperative relationships among themselves or with third parties to increase the ability of their products or services to address the needs of our current and prospective clients.

Our Chief Executive Officer is critical to our business.

Our future success largely depends upon the continued service of our Chief Executive Officer. The services of Michael W. Ferro, Jr., our founder, Chairman of the Board of Directors and Chief Executive Officer would be very difficult to replace.

If we fail to protect our intellectual property rights or face a claim of intellectual property infringement by a third party, we could lose our intellectual property rights or be liable for significant damages.

Our success depends significantly upon our proprietary technology. We have a limited number of patents, and no plans to initiate applications for any new patents. Unauthorized parties could copy aspects of our products or services or obtain and use information that we regard as proprietary. Our means of protecting our proprietary rights may not be adequate, and our competitors may independently develop similar technology or duplicate our products or our other intellectual property rights. Our failure to protect our proprietary rights adequately, or our competitors' successful duplication of our technology, could negatively affect our operating results and cause the price of our common stock to decline.

In addition, we have agreed, and may agree in the future, to indemnify certain of our customers against claims that our software infringes upon the intellectual property rights of others. We could incur substantial costs in defending ourselves and our customers against infringement claims. In the event of a claim of infringement, we and our customers could be required to obtain one or more licenses from third parties. We or our customers may be unable to obtain necessary licenses from third parties at a reasonable cost, or at all. Defense of any lawsuit or failure to obtain any such required licenses could harm our business, operating results and financial condition.

Litigation over intellectual property rights could disrupt or otherwise have a negative impact on our business.

There has been frequent litigation in the computer industry regarding intellectual property rights. Third parties may make claims of infringement by us with respect to current or future products, trademarks or other proprietary rights. These claims could be time-consuming, result in costly litigation, divert management's attention, cause product release or service delays, require us to redesign our products or services or require us to enter into costly royalty or licensing agreements. Any of these events could have a materially adverse effect on our financial condition and results of operations.

If we become subject to product liability litigation, it could be costly and time consuming to defend.

Since our products are used for company-wide, integral computer applications with significant potential impact on our customers' sales of their products, any errors, defects or other performance problems with our products could result in financial or other loss for our customers. Although we have contractual limits to our liability, product liability litigation would be time consuming and costly to defend, even if we were successful.

We are subject to NASDAQ regulations that require us to maintain minimum stock prices and levels of stockholders' equity and free float market capitalization that must be met to satisfy the listing requirements of the NASDAQ National Market. If we are unable to meet such requirements, our stock may be delisted which could cause the stock price to decline and reduce the ability of stockholders to purchase or sell shares of the Company's stock.

Twice in the past two years, the Company has failed to comply with the minimum share price or required equity levels for continued listing by the NASDAQ National Market. When those events occurred, the NASDAQ required the Company to immediately implement a plan to ensure compliance with such regulations. Although the Company was successful in implementing these compliance plans, there is no assurance that such situations may not occur in the future. In addition, significant losses could cause a reduction in stockholders' equity below the minimum standards required to maintain listing on the NASDAQ National Market. If the Company's stock were delisted by NASDAQ, such a delisting could substantially limit the ability of stockholders to purchase or sell shares of the Company's stock and could lower the market value of such stock.

Risks Related to Our Industry

We are highly dependent on the acceptance and effectiveness of the Internet as a medium for business-to-business commerce.

Our future revenues and the success of a number of our products and services are dependent in large part on an increase in the use of the Internet for business-to-business commerce. The failure of the Internet to continue to develop as a commercial or business medium could harm our business, operating results and financial condition. The acceptance and use of the Internet for business-to-business commerce could be limited by a number of factors, such as the growth and the use of the Internet in general, the threat of illegal activity that causes performance degradations at unprotected sites across the Internet, the relative ease of conducting business on the Internet, the efficiencies and improvements that conducting commerce on the Internet provides, concerns about transaction security and taxation of transactions on the Internet.

We depend on the speed and reliability of the Internet.

The recent growth in Internet traffic has caused frequent periods of decreased performance. If Internet usage continues to grow rapidly, its infrastructure may not be able to support these demands and its performance and reliability may decline. Decreased performance at some unprotected Internet sites has also been attributed to illegal attacks by third parties. If outages or delays on the Internet occur frequently or increase in frequency, or businesses are not able to protect themselves adequately from such illegal attacks, business-to-business e-commerce could grow more slowly or decline, which might reduce the demand for our software products and services. The ability of our products to satisfy our customers' needs is ultimately limited by and depends upon the speed and reliability of the Internet. Consequently, the emergence and growth of the market for our software products and services depends upon improvements being made to the entire Internet to alleviate overloading and congestion. If these improvements are not made, the ability of our customers to benefit from our products and services will be hindered, and our business, operating results and financial condition could suffer.

Increased security risks of the Internet may deter future use of our software products and services.

A fundamental requirement of Internet-based, business-to-business software is the secure transmission of confidential information over public networks. Advances in computer capabilities, new discoveries in the field of cryptography, or other developments might result in a compromise or a breach of the security features contained in our software or the algorithms used by our customers and their business partners to protect content and transactions on Internet e-commerce marketplaces or proprietary information in our customers' and their business partners' databases. Anyone who is able to

circumvent security measures could misappropriate proprietary, confidential customer information or cause interruptions in our customers' and their business partners' operations. Our customers and their business partners may be required to incur significant costs to protect against security breaches or to alleviate problems caused by breaches, reducing the demand for our software products and services. Further, a well-publicized compromise of security could deter businesses from using the Internet to conduct transactions that involve transmitting confidential information. The failure of the security features of our software to prevent security breaches, or well-publicized security breaches affecting the Internet in general, could significantly harm our business, operating results and financial condition.

Internet-related laws could adversely affect our business.

Regulation of the Internet is largely unsettled. The adoption of laws, regulations or taxes that increase the costs or administrative burdens of doing business using the Internet could cause companies to seek an alternative means of transacting business. If the adoption of new Internet laws, regulations or taxes causes companies to seek alternative methods for conducting business, the demand for our software products and services could decrease and our business could be adversely affected.

FORWARD-LOOKING STATEMENTS

This prospectus, including the documents incorporated by reference herein, contain forward-looking statements that are based on current expectations, estimates and projections. Words such as "anticipates", "believes", "continues", "estimates", "expects", "forecasts", "goal", "intends", "may", "opportunity", "plans", "potential", "project", "should", "seeks", "targets" and "will", and variations of these words and similar expressions, are intended to identify forward-looking statements. These statements are not guarantees of future performance and involve risks, uncertainties and assumptions that are difficult to predict and could cause actual results to differ materially from those expressed, implied or forecasted in the forward-looking statements. Forward-looking statements are based upon assumptions as to future events that may not prove to be accurate. These risks and uncertainties include, among others, those described in "Risk Factors" and elsewhere in this prospectus. Except as required by law, we undertake no obligation to update any forward-looking statement, whether as a result of new information, future events or otherwise.

USE OF PROCEEDS

We will not receive any of the proceeds from the sale of the common stock offered under this prospectus.

DIVIDEND POLICY

On May 1, 2003, we announced that our Board of Directors had declared a special cash dividend in the amount of $2.50 per share of our common stock ("Special Dividend"). The Special Dividend was paid on June 4, 2003 to stockholders of record as of May 20, 2003. As of May 20, 2003, we had 8,136,643 shares of common stock outstanding, which resulted in a total Special Dividend payment of approximately $20,342,000. Previous to the declaration and payment of the Special Dividend, we had never declared or paid any cash dividends on our common stock. We currently intend to retain earnings, if any, to support our growth strategy and do not anticipate paying further cash dividends in the foreseeable future.

DESCRIPTION OF CAPITAL STOCK

General

Our authorized capital stock consists of 75,000,000 shares of common stock, par value $0.001 per share and 5,000,000 shares of undesignated preferred stock, par value $0.001 per share.

The following description of our capital stock is intended as a summary only and is qualified in its entirety by reference to our amended and restated certificate of incorporation and amended and restated by-laws and to Delaware corporate law. We refer in this section to our amended and restated certificate of incorporation as our "Certificate" and we refer to our amended and restated by-laws as our "Bylaws."

Common Stock

Holders of common stock are entitled to one vote per share on all matters on which the holders of common stock are entitled to vote and do not have any cumulative voting rights. Holders of common stock have no preemptive, conversion, redemption or sinking fund rights. Holders of common stock are entitled to receive dividends as may from time to time be declared by our Board of Directors out of funds legally available therefore. Except for the special dividend described herein, we have never paid or declared any cash dividends on our common stock or other securities and do not anticipate paying cash dividends in the foreseeable future. In the event of a liquidation, dissolution or winding up of Click Commerce, holders of common stock are entitled to share equally and ratably in the assets of Click Commerce, if any, remaining after the payment of all our liabilities and the liquidation preference of any then outstanding class or series of preferred stock. The outstanding shares of common stock are fully paid and nonassessable. The rights, preferences and privileges of holders of common stock are subject to any series of preferred stock that we may issue in the future, as described below.

Undesignated Preferred Stock

Our Board of Directors is authorized, without further Stockholder approval, to issue from time to time up to an aggregate of 5,000,000 shares of preferred stock in one or more series and to fix or alter the designations, preferences, rights, dividend rates, and any qualifications, limitations or restrictions of the shares of any series thereof, including the dividend rates, conversion rights or restrictions of the shares of any series thereof, including the dividend rights dividend rates, conversion rights, voting rights, terms of redemption including sinking fund provisions, redemption price or prices, liquidation preferences and the number of shares constituting any series or designations of any series. The issuance of preferred stock by our Board of Directors could adversely affect the rights of holders of common stock. Immediately after this offering, the will be no shares of preferred stock outstanding, and we have no present plans to issue any shares of preferred stock. See "—Anti-Takeover Effects of Delaware Law and our Certificate and Bylaws."

Listing

Our common stock is listed on the NASDAQ National Market under the symbol "CKCM". The shares of common stock being offered in this prospectus have been approved for listing, subject to official notice of issuance.

Anti-Takeover Effects of Delaware Law and Our Certificate and Bylaws

We are subject to the provisions of Section 203 of the Delaware General Corporation Law, as amended, or DGCL. Subject to a number of exceptions, Section 203 of the DGCL prohibits a publicly-held Delaware corporation from engaging in a "business combination" with an "interested stockholder" for a period of three years after the date of the transaction in which the person became

an interested stockholder, unless the interested stockholder attained status as an interested stockholder with the approval of the Board of Directors or unless the business combination is approved in a prescribed manner. A "business combination" includes mergers, asset sales and other transactions resulting in a financial benefit to the interested stockholder. Subject to exceptions, an "interested stockholder" is a person who, together with affiliates and associates, owns, or within three years did own, 15% or more of a corporation's voting stock. This statute could prohibit or delay the accomplishment of mergers or other takeover or change in control attempts with respect to our Company and, accordingly, may discourage attempts to acquire us.

In addition, a number of provisions of the Certificate and Bylaws, which provisions are summarized in the following paragraphs, may be deemed to have an anti-takeover effect and may delay, defer or prevent a tender offer or takeover attempt that a stockholder might consider in its best interest, including those attempts that might result in a premium over the market price for the shares held by our stockholders.

Board of Directors Vacancies; Classified Board. Following this offering, our Board of Directors will be divided into three classes, each of whose members will serve for a staggered three-year term. The Certificate also authorizes our Board of Directors to fill vacant directorships or increase the size of the Board of Directors. These provisions may deter a stockholder from removing incumbent directors and simultaneously gaining control of the Board of Directors by filling the vacancies created by removal with its own nominees.

Stockholder Action; Special Meeting of Stockholders. The Certificate and Bylaws provide that stockholders may not take action by written consent, but only at a duly called annual or special meeting of stockholders. The Certificate and Bylaws further provide that special meetings of stockholders of our Company may be called only by the Chairman of the Board of Directors or a majority of the Board of Directors or by a committee of the Board of Directors which has been duly designated by the Board of Directors and whose powers and authority, as provided in a resolution of the Board of Directors or in the Bylaws of the Company, include the power to call such meetings.

Advance Notice Requirements for Stockholder Proposals and Director Nominations. The Bylaws provide that stockholders seeking to bring business before an annual meeting of stockholders, or to nominate candidates for election as directors at an annual meeting of stockholders, must provide timely notice thereof in writing. To be timely, a stockholder's notice must be delivered to the secretary at our principal executive offices not less than 120 days prior to the first anniversary of the date the corporation's proxy statement was released to security holders in connection with the preceding year's annual meeting of stockholders; provided, that if no annual meeting of stockholders was held in the previous year or the date of the annual meeting of stockholders has been changed by more than 30 calendar days from the date contemplated at the time of the previous year's proxy statement, a proposal shall be received by the corporation no later than ten days following the day on which notice of the date of the meeting was mailed or public announcement of the date of the meeting was made, whichever comes first. In the case of a special meeting of stockholders, notice by the stockholder, to be timely, must be so received not more than 90 days nor later than the later of (1) 60 days prior to the special meeting of stockholders or (2) the close of business on the 10th day following the date on which public announcement is first made of the date of the special meeting and of the nominees proposed by the Board of Directors to be elected at such meeting. The Bylaws also specify requirements as to the form and content of a stockholder's notice. These provisions may preclude stockholders from bringing matters before an annual meeting of stockholders or from making nominations for directors at an annual meeting of stockholders.

Authorized But Unissued Shares. The authorized but unissued shares of common stock and preferred stock are available for future issuance without stockholder approval, subject to limitations imposed by the NASDAQ National Market. These additional shares may be utilized for a variety of

corporate purposes, including future public offerings to raise additional capital, corporate acquisitions and employee benefit plans. The existence of authorized but unissued and unreserved common stock and preferred stock could render more difficult or discourage an attempt to obtain control of our Company by means of a proxy contest, tender offer, merger or otherwise.

The DGCL provides generally that the affirmative vote of a majority of the shares entitled to vote on any matter is required to amend a corporation's certificate of incorporation or bylaws, unless a corporation's certificate of incorporation or bylaws, as the case may be, requires a greater percentage. We have provisions in our Certificate and Bylaws that require a super-majority vote of the stockholders to amend, revise or repeal provisions that may have an anti-takeover effect.

Limitation of Liability and Indemnification

The Certificate includes provisions to (1) eliminate the personal liability of our Directors for monetary damages resulting from breaches of their fiduciary duty to the extent permitted by the DGCL and (2) indemnify our Directors and officers to the fullest extent permitted by the DGCL, including circumstances in which indemnification is otherwise discretionary.

We have entered into agreements to indemnify each of our Directors and some of our executive officers, in addition to the indemnification provided for in the Bylaws. We believe that these provisions and agreements are necessary to attract and retain qualified directors and officers. Our Bylaws also permit us to secure insurance on behalf of any officer, director, employee or other agent for any liability arising out of his or her actions, regardless of whether the DGCL would permit indemnification.

Transfer Agent and Registrar

The transfer agent and registrar for our common stock is Computershare Investor Services LLC.

MATERIAL U.S. FEDERAL TAX
CONSIDERATIONS FOR NON-U.S. HOLDERS

General

The following is a general discussion of certain United States federal income and estate tax consequences of the ownership and disposition of our common stock by a Non-U.S. holder. Generally, for purposes of this discussion, a "Non-U.S. holder" is a beneficial owner of our common stock who or which is, for United States federal income tax purposes, a non-resident alien individual, a foreign corporation, or a foreign estate or trust. In general, an individual is a non-resident alien individual with respect to a calendar year if he or she is not a United States citizen (and in certain circumstances is not a former United States citizen) and, with respect to such calendar year (i) has at no time had the privilege of residing permanently in the United States and (ii) is not present in the United States a specified number of days in the current year and the prior two years. Different rules apply for United States federal estate tax purposes. We refer you to "—Federal Estate Taxes" below.

The following discussion is based upon current provisions of the Internal Revenue Code of 1986, as amended (the "Code"), existing, proposed and temporary regulations promulgated under the Code and administrative and judicial interpretations, all of which are subject to change, possibly on a retroactive basis. The following discussion does not address aspects of United States federal taxation other than income and estate taxation, and does not address all aspects of United States federal income and estate taxation. The discussion does not consider any specific facts or circumstances that might apply to a particular Non-U.S. holder and does not address all aspects of United States federal income and estate tax law that might be relevant to a Non-U.S. holder subject to special treatment under the Code, for example, insurance companies, tax-exempt organizations, financial institutions or broker-dealers. This discussion does not address the tax treatment of partnerships or persons who hold their interests through a partnership or other pass-through entity. In addition, this discussion does not address state, local or non-United States tax consequences that might be relevant to a Non-U.S. holder, and does not address the applicability or effect of any specific tax treaty. Accordingly, prospective purchasers of our common stock are urged to consult their tax advisors regarding the United States federal, state and local tax consequences, as well as non-United States tax consequences, of acquiring, holding and disposing of shares of our common stock.

Dividends

In general, if we were to make distributions with respect to our common stock, such distributions would be treated as dividends to the extent of our current or accumulated earnings and profits as determined under the Code. Any distribution that is not a dividend will be applied in reduction of the Non-U.S. holder's basis in our common stock. To the extent the distribution exceeds such basis, the excess will be treated as gain from the disposition of our common stock.

Subject to the discussion below, dividends paid to a Non-U.S. holder of our common stock generally will be subject to withholding of United States federal income tax at a 30% rate. A lower rate may apply if the Non-U.S. holder is a qualified tax resident of a country with which the U.S. has an income tax treaty and if certain procedural requirements are satisfied by the Non-U.S. holder. A Non- U.S. holder generally will have to file IRS Form W-8BEN or successor form in order to be eligible to claim the benefits of a U.S. income tax treaty. Special rules may apply in the case of dividends paid to or through an account maintained outside the United States at a financial institution, for which certain documentary evidence procedures must be followed.

Withholding generally will not apply in respect of dividends if (i) the dividends are effectively connected with the conduct of a trade or business of the Non-U.S. holder within the United States or (ii) a tax treaty applies, the dividends are effectively connected with the conduct of a trade or business of the Non-U.S. Holder within the United States and are attributable to a United States permanent

establishment (or a fixed base through which certain personal services are performed) maintained by the Non-U.S. holder. To claim relief from withholding on this basis, a Non-U.S. Holder generally must file IRS Form W-8ECI or successor form, with the payor of the dividend.

Dividends received by a Non-U.S. holder that are effectively connected with the conduct of a trade or business within the United States or, if a tax treaty applies, are effectively connected with the conduct of a trade or business within the United States and attributable to a United States permanent establishment (or a fixed base through which certain personal services are performed), are subject to United States federal income tax on a net income basis (that is, after allowance for applicable deductions) at applicable graduated individual or corporate rates. Any such dividends received by a Non-U.S. holder that is a corporation may, under certain circumstances, be subject to an additional "branch profits tax" at a 30% rate or such lower rate as may be specified by an applicable income tax treaty.

A Non-U.S. holder eligible for a reduced rate of withholding of United States federal income tax may obtain a refund of any excess amounts withheld by timely filing an appropriate claim for refund with the United States Internal Revenue Service.

Gain on Disposition of Common Stock

A Non-U.S. holder generally will not be subject to United States federal income tax with respect to gain recognized on a sale, exchange, or other disposition of our common stock (including a redemption of our common stock treated as a sale for federal income tax purposes) unless (i) the gain is effectively connected with the conduct of a United States trade or business of the Non-U.S. holder, (ii) the Non-U.S. holder is an individual who holds our common stock as a capital asset, is present in the United States for 183 or more days in the taxable year of the sale or other disposition, and either the individual has a "tax home" in the United States or the sale is attributable to an office or other fixed place of business maintained by the individual in the United States, (iii) the Non-U.S. holder is subject to tax under U.S. tax law provisions applicable to certain U.S. expatriates (including former citizens or residents of the United States), or (iv) we are or have been a "United States real property holding corporation" within the meaning of Section 897(c)(2) of the Code at any time within the shorter of the five-year period ending on the date of disposition or the Non-U.S. holder's holding period and certain other conditions are met. We do not believe that we are, or are likely to become, a "United States real property holding corporation".

The 183-day rule summarized above applies only in limited circumstances because generally an individual present in the United States for 183 days or more in the taxable year of the sale, exchange, or other disposition will be treated as a resident for United States federal income tax purposes and therefore will be subject to United States federal income tax at graduated rates applicable to individuals who are United States persons for such purposes.

Non-U.S. holders should consult applicable tax treaties, which may result in United States federal income tax treatment on the sale, exchange or other disposition of the common stock different from that described above.

Backup Withholding Tax and Information Reporting

We must report annually to the IRS and to each Non-U.S. holder any dividend income that is subject to withholding, or that is exempt from U.S. withholding tax pursuant to a tax treaty. Copies of these information returns may also be made available under the provisions of a specific treaty or agreement to the tax authorities of the country in which the Non-U.S. holder resides.

A Non-U.S. holder of common stock that fails to establish that it is entitled to an exemption or to provide a correct taxpayer identification number and other information to the payor in accordance with

applicable U.S. Treasury regulations may be subject to information reporting and backup withholding on payments of dividends. The rate of backup withholding is currently 28%. Backup withholding may apply to the payment of disposition proceeds by or through a non-U.S. office of a broker that is a U.S. person or a "U.S. related person" unless certification requirements are established or an exemption is otherwise established and the broker has no actual knowledge that the holder is a U.S. person.

The payment of proceeds from the disposition of common stock to or through the United States office of any broker, U.S. or foreign, will be subject to information reporting and possible backup withholding unless the owner certifies as to its non-U.S. status under penalty of perjury or otherwise establishes its entitlement to an exemption from information reporting and backup withholding, provided that the broker does not have actual knowledge that the holder is a U.S. person or that the conditions of an exemption are not, in fact, satisfied. The payment of proceeds from the disposition of common stock to or through a non-U.S. office of a non-U.S. broker that is not a "U.S. related person" will not be subject to information reporting or backup withholding. For this purpose, a "U.S. related person" is a foreign person with one or more enumerated relationships with the United States.

In the case of the payment of proceeds from the disposition of common stock to or through a non-U.S. office of a broker that is either a U.S. person or a U.S. related person, the regulations require information reporting (but not backup withholding) on the payment unless the broker has documentary evidence in its files that the owner is a Non-U.S. holder and the broker has no knowledge to the contrary.

Any amounts withheld under the backup withholding rules from a payment to a Non-U.S. holder will be allowed as a refund or a credit against such Non-U.S. holder's U.S. federal income tax liability provided the requisite procedures are followed.

Federal Estate Taxes

An individual Non-U.S. holder who is treated as the owner of our common stock at the time of his death generally will be required to include the value of such common stock in his gross estate for United States federal estate tax purposes and may be subject to United States federal estate tax on such value, unless an applicable tax treaty provides otherwise. For United States federal estate tax purposes, a "Non-U.S. holder" is an individual who is neither a citizen nor a domiciliary of the United States. In general, an individual acquires a domicile in the United States for United States estate tax purposes by living in the United States, for even a brief period of time, with the intention of remaining in the United States indefinitely.

SELLING STOCKHOLDERS

The following table sets forth the name of each selling stockholder and:

•: the number of shares of our common stock that will be beneficially owned by each selling stockholder upon issuance pursuant to the terms of the Agreement and Plan of Merger among Click Commerce, Inc., Click Texas Corp., bTrade Acquisition Corp., bTrade, Inc. and Certain Stockholders of bTrade Inc., dated June 17, 2004 (the "bTrade Merger Agreement"); and
•: the amount and percentage of our common stock to be beneficially owned by each selling stockholder assuming the sale of all shares of common stock that the selling stockholder may sell under this prospectus.

The following table is based on information supplied to us by the selling stockholders. We have determined beneficial ownership in accordance with the rules of the SEC. Unless otherwise indicated, the persons and entities included in the table have sole voting and investment power with respect to all shares beneficially owned, except to the extent authority is shared by spouses under applicable law. The table lists applicable percentage ownership based on 9,726,135 shares outstanding, which is based upon the sum of 9,027,737 shares outstanding as of September 10, 2004 and 698,398 shares of common stock to be issued pursuant to the bTrade Merger Agreement.

Stockholder	Number of Shares of Common Stock Beneficially Owned Before the Offering	Percentage Ownership		Maximum Number of Shares of Common Stock Offered
Hunt Capital Growth Fund II, L.P. (1)	233,268	2.40	%	233,268
Shawmut Equity Partners, L.P. (2)	150,891	1.55		150,891
The Productivity Fund IV, L.P. (3)	108,199	1.11		108,199
First Analysis Infrastructure and Environmental Private Equity Fund III, L.P. (4)	44,929	*		44,929
David Lonsdale (5)	32,483	*		32,483
Stephen Lynn (6)	27,500	*		27,500
Kevin Stadler (6)	27,500	*		27,500
CMS Co-Investment Subpartnership (7)	22,494	*		22,494
First Analysis Environmental and Information Technology Private Equity Fund III (8)	11,233	*		11,233
Hook Communications Partners, L.P. (9)	10,928	*		10,928
James Taylor (10)	10,000	*		10,000
The Productivity Fund IV Advisors Fund, L.P. (11)	4,162	*		4,162
Hook Partners III L.L.C. (12)	3,643	*		3,643
Bret R. Maxwell (13)	3,615			3,615
Dwayne Walker (14)	2,602	*		2,602
K.B. and Sukanya Chandrasekhar Trust (15)	2,382	*		2,382
Gunnar Overstrom (16)	972	*		972
Beyond Ventures (16)	971	*		971
WS Investment Co. 2000A (17)	563	*		563
Michael J. Danaher (18)	63	*		63
Total for selling stockholders	698,398	7.18	%	698,398

*: Denotes that the selling stockholder owns less than 1% of our common stock prior to the offering. No selling stockholder will own more than 1% of our common stock after the offering.

(1): Includes 23,326 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(2): Includes 15,089 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(3): Includes 10,819 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(4): Includes 4,492 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(5): Includes 3,248 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(6): Includes 2,750 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(7): Includes 2,249 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(8): Includes 1,123 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(9): Includes 1,092 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(10): Includes 1,000 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(11): Includes 416 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(12): Includes 364 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(13): Includes 361 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(14): Includes 260 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(15): Includes 238 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(16): Includes 97 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(17): Includes 56 shares currently held in escrow pursuant to the bTrade Merger Agreement.
(18): Includes 6 shares currently held in escrow pursuant to the bTrade Merger Agreement.

PLAN OF DISTRIBUTION

The Selling Stockholders, and their pledgees, donees, transferees or other successors in interest, may from time to time offer and sell, separately or together, some or all of the shares of common stock covered by this prospectus. Registration of shares of common stock covered by this prospectus does not mean, however, that those shares of common stock necessarily will be offered or sold.

The shares of common stock covered by this prospectus may be sold from time to time, at market prices prevailing at the time of sale, at prices related to market prices, at a fixed price or prices subject to change or at negotiated prices, by a variety of methods including the following:

•: on the NASDAQ National Market (including through at the market offerings);
•: in the over-the-counter market;
•: in privately negotiated transactions;
•: through broker-dealers, who may act as agents or principals;
•: through one or more underwriters on a firm commitment or best-efforts basis;
•: in a block trade in which a broker-dealer will attempt to sell a block of shares of common stock as agent but may position and resell a portion of the block as principal to facilitate the transaction;
•: through put or call option transactions relating to the common stock;
•: directly to one or more purchasers;
•: through agents; or
•: in any combination of the above.

In effecting sales, brokers or dealers engaged by the selling stockholders may arrange for other brokers or dealers to participate. Broker-dealer transactions may include:

•: purchases of shares of the common stock by a broker-dealer as principal and resales of shares of the common stock by the broker-dealer for its account pursuant to this prospectus;
•: ordinary brokerage transactions; or
•: transactions in which the broker-dealer solicits purchasers on a best efforts basis.

Neither we nor the selling stockholders have entered into any agreements, understandings or arrangements with any underwriters or broker-dealers regarding the sale of shares of common stock covered by this prospectus. At any time a particular offer of the shares of common stock covered by this prospectus is made, a revised prospectus or prospectus supplement, if required, will be distributed which will set forth the aggregate amount of shares of common stock covered by this prospectus being offered and the terms of the offering, including the name or names of any underwriters, dealers, brokers or agents. In addition, to the extent required, any discounts, commissions, concessions and other items constituting underwriters' or agents' compensation, as well as any discounts, commissions or concessions allowed or reallowed or paid to dealers, will be set forth in such revised prospectus supplement. Any such required prospectus or prospectus supplement, and, if necessary, a post-effective amendment to the registration statement of which this prospectus is a part, will be filed with the SEC to reflect the disclosure of additional information with respect to the distribution of the shares of common stock covered by this prospectus.

The selling stockholders may also authorize agents or underwriters to solicit offers by certain types of institutional investors to purchase securities at the public offering price set forth in the revised prospectus or prospectus supplement pursuant to delayed delivery contracts providing for payment and

delivery on a specified date in the future. The conditions to these contracts and the commission that the selling stockholders must pay for solicitation of these contracts will be described in a revised prospectus or prospectus supplement.

In connection with the sale of the shares of common stock covered by this prospectus through underwriters, underwriters may receive compensation in the form of underwriting discounts or commissions and may also receive commissions from purchasers of shares of common stock for whom they may act as agent. Underwriters may sell to or through dealers, and such dealers may receive compensation in the form of discounts, concessions or commissions from the underwriters and/or commissions from the purchasers for whom they may act as agent.

Any underwriters, broker-dealers or agents participating in the distribution of the shares of common stock covered by this prospectus may be deemed to be "underwriters" within the meaning of the Securities Act of 1933 (the "Securities Act"), and any commissions received by any of those underwriters, broker-dealers or agents may be deemed to be underwriting commissions under the Securities Act.

We estimate that the total expenses in connection with the offer and sale of shares of common stock pursuant to this prospectus, other than underwriting discounts and commissions, will be approximately $55,431.79, including fees of our counsel and accountants, fees payable to the SEC and listing fees. We will pay these expenses.

We and the selling stockholders may agree to indemnify underwriters, broker-dealers or agents against certain liabilities, including liabilities under the Securities Act, and may also agree to contribute to payments which the underwriters, broker-dealers or agents may be required to make.

Certain of the underwriters, broker-dealers or agents who may become involved in the sale of the shares of common stock covered by this prospectus may engage in transactions with and perform other services for us in the ordinary course of their business for which they receive customary compensation.

Some of the shares of common stock covered by this prospectus may be sold by selling stockholders in private transactions or under Rule 144 under the Securities Act rather than pursuant to this prospectus.

WHERE YOU CAN FIND MORE INFORMATION

You may read and copy materials that we have filed with the SEC at the SEC's public reference room located at 450 Fifth Street, N.W. Room 1024, Washington, D.C. 20549. Please call the SEC at 1-800-SEC-0330 for further information on the public reference room. Our filings with the SEC are also available on the Internet at the SEC's website at www.sec.gov.

You may also request a copy of each document incorporated by reference in this prospectus at no cost, by writing or calling us at the following address or telephone number:

200 East Randolph Drive, 52nd Floor
Chicago, Illinois 60601
Attention: Investor Relations
(312)-482-9006

Exhibits to a document will not be provided unless they are specifically incorporated by reference in that document.

INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE

We file annual, quarterly and current reports, proxy statements and other information with the SEC. Some of the information that you may want to consider in deciding whether to invest in the shares of common stock is not included in this prospectus, but rather is incorporated by reference to documents that we have filed with the SEC. This permits us to disclose important information to you by referring to those filings rather than repeating them in full in this prospectus. The information incorporated by reference in this prospectus contains important business and financial information. In addition, information that we file with the SEC after the date of this prospectus and prior to the completion of this offering will update and may supersede the information contained in this prospectus and incorporated filings. We specifically incorporate by reference the following documents filed by us with the SEC:

(1): Annual Report on Form 10-K for the fiscal year ended December 31, 2003, filed on March 30, 2004.
(2): Quarterly Report on Form 10-Q for the quarter ended March 31, 2004, filed on May 17, 2004.
(3): Quarterly Report on Form 10-Q for the quarter ended June 30, 2004, filed on August 16, 2004.
(4): Current Reports on Form 8-K filed on March 5, 2004, April 23, 2004 and July 6, 2004.

All documents filed by us under Section 13(a), 13(c), 14 or 15(d) of the Securities Exchange Act of 1934 prior to the termination of the offering to which this prospectus relates shall be deemed to be incorporated by reference.

Any statement contained in this prospectus or any document incorporated by reference in this prospectus shall be deemed to be modified or superseded for purposes of this prospectus to the extent that a statement contained herein, or in any other subsequently filed document which is also incorporated by reference into this prospectus, modifies or supersedes such statement. Any such statement so modified or superseded shall not be deemed, except as so modified or superseded, to constitute a part of this prospectus. Statements contained in this prospectus as to the contents of any contract or other document referred to in this prospectus do not purport to be complete, and where reference is made to the particular provisions of such contract or other document, such statements are qualified in all respects by all of the provisions of such contract or other document. Information which is furnished but not filed with the SEC shall not be incorporated by reference in this prospectus.

LEGAL MATTERS

McDermott Will & Emery LLP, Chicago, Illinois, will pass upon the validity of the shares of common stock offered hereby.

EXPERTS

The consolidated financial statements of Click Commerce, Inc. and subsidiaries as of December 31, 2003 and 2002 and for each of the years in the three year period ended December 31, 2003 and for the consolidated financial statement schedule for the three year period ended December 31, 2003 have been incorporated by reference in this prospectus in reliance upon reports of KPMG LLP, independent certified public accountants, incorporated by reference herein, and upon the authority of said firm as experts in accounting and auditing. incorporated in this prospectus by reference to the Form 10-K filed March 30, 2004, have been audited by KPMG LLP, independent auditors, as set forth in their report therein, and are incorporated by reference in reliance upon such report given on the authority of such firm as experts in accounting and auditing.

PART II

INFORMATION NOT REQUIRED IN THIS PROSPECTUS

Item 14. Other Expenses of Issuance and Distribution

The following table sets forth the various expenses in connection with the sale and distribution of securities being registered, other than discounts, concessions and brokerage commissions.

SEC registration fee		$	431.79
Legal fees and expenses			25,000.00	*
Accounting fees and expenses			15,000.00	*
Miscellaneous			15,000.00	*

	Total	$	55,431.79

*: Estimated

Item 15. Indemnification of Directors and Officers

Our Certificate in effect as of the date hereof provides that, except to the extent prohibited by the Delaware General Corporation Law, as amended (the "DGCL"), our Directors shall not be personally liable to us or our stockholders for monetary damages for any breach of fiduciary duty as Directors. Under the DGCL, our Directors have a fiduciary duty to us which is not eliminated by this provision of the Certificate and, in appropriate circumstances, equitable remedies such as injunctive or other forms of non-monetary relief will remain available. In addition, each director will continue to be subject to liability under the DGCL for breach of the director's duty of loyalty to us, for acts or omissions which are found by a court of competent jurisdiction to be not in good faith or involving intentional misconduct, for knowing violations of law, for actions leading to improper personal benefit to the director, and for payment of dividends or approval of stock repurchases or redemptions that are prohibited by the DGCL. This provision also does not affect the Directors' responsibilities under any other laws, such as the Federal securities laws. We have obtained, and may continue to obtain, liability insurance for our officers and directors.

Section 145 of the DGCL empowers a corporation to indemnify its directors and officers and to purchase insurance with respect to liability arising out of their capacity or status as directors and officers, provided that this provision shall not eliminate or limit the liability of a director: (i) for any breach of the director's duty of loyalty to the corporation or its stockholders, (ii) for acts or omissions not in good faith or which involve intentional misconduct or a knowing violation of law, (iii) arising under Section 174 of the DGCL, or (iv) for any transaction from which the director derived an improper personal benefit. The DGCL provides further that the indemnification permitted thereunder shall not be deemed exclusive of any other rights to which the directors and officers may be entitled under the corporation's bylaws, any agreement, a vote of stockholders or otherwise. The Certificate eliminates the personal liability of directors to the fullest extent permitted by Section 102(b)(7) of the DGCL and provides that we may fully indemnify any person who was or is a party or is threatened to be made a party to any threatened, pending or completed action, suit or proceeding (whether civil, criminal, administrative or investigative) by reason of the fact that such person is or was a director or officer of this corporation, or is or was serving at our request as a director or officer of another corporation, partnership, joint venture, trust, employee benefit plan or other enterprise, against expenses (including attorney's fees), judgments, fines and amounts paid in settlement actually and reasonably incurred by such person in connection with such action, suit or proceeding.

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Item 16. Exhibits

Exhibit		Description of Exhibit
2.1		Agreement and Plan of Merger, dated as of March 21, 2003, by and among Click Commerce, Inc., Allegis Acquisition, Inc., Allegis Acquisition of California, Inc. and Allegis Corporation (incorporated by reference to Exhibit 2.1 to Click Commerce, Inc.'s Form 8-K filed March 28, 2003).
2.2		Asset Purchase Agreement, dated as of March 17, 2004, by and among Click Commerce, Inc., Click West Coast Corp, Click-Webridge, Inc., and Webridge, Inc. (incorporated by reference to Exhibit 2.1 to Click Commerce, Inc.'s Form 8-K filed April 23, 2004).
2.3		First Amendment to Asset Purchase Agreement, dated as of March 30, 2004, by and among Click Commerce, Inc., Click West Coast Corp, Click-Webridge, Inc., and Webridge, Inc. (incorporated by reference to Exhibit 2.2 to Click Commerce, Inc.'s Form 8-K filed April 23, 2004).
2.4		Agreement and Plan of Merger, dated as of June 17, 2004, by and among the Click Commerce, Inc., Click Texas Corp, bTrade Acquisition Corp., bTrade, Inc. and certain stockholders of bTrade, Inc. (incorporated by reference to Exhibit 2.1 to Click Commerce, Inc.'s Form 8-K filed July 6, 2004).
4.1		Specimen Common Stock Certificate of the Registrant (incorporated herein by reference to Exhibit 4.1 to Click Commerce, Inc.'s Registration Statement on Form S-1, as amended, Registration No. 333-30564).
5.1		Opinion of McDermott Will & Emery LLP.*
23.1		Consent of KPMG LLP.
23.2		Consent of Grant Thornton LLP
23.3		Consent of McDermott Will & Emery LLP (incorporated by reference into Exhibit 5.1).*
24.1		Power of Attorney (included on signature page of the Form S-3).

*: To be filed by amendment

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;

(ii) To reflect in the prospectus any facts or events arising after the effective date of the 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 the registration statement. Notwithstanding the foregoing, any increase or decrease in 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 that a 20 percent change in the maximum aggregate offering price set forth in the "Calculation of Registration Fee" table in the effective registration statement; and

II-2

(iii) To include any material information with respect to the plan of distribution not previously disclosed in the registration statement or any material change to such information in the registration statement; Provided, however, that paragraphs 1 (i) and (ii) do not apply if the registration statement is on Form S-3 or Form S-8 or Form F-3, and the information required to be included in a post-effective amendment by those paragraphs is contained in periodic reports filed with or furnished to the Commission by the registrant pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 that are incorporated by reference in the registration statement.

(2) That, for the purpose of determining any liability under the Securities Act of 1933, each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that 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 undersigned registrant hereby undertakes that, for purposes of determining any liability under the Securities Act of 1933, each filing of the Registrant's annual report pursuant to Section 13(a) or Section 15(d) of the Securities Exchange Act of 1934 (and, where applicable, each filing of an employee benefit plan's annual report pursuant to Section 15(d) of the Securities Exchange Act of 1934) that is incorporated by reference in the registration statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be permitted to directors, officers and controlling persons of the registrant pursuant to the provisions described in Item 15, or otherwise, the registrant has been advised that in the opinion of the SEC such indemnification is against public policy as expressed in the 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 of whether such indemnification by it is against public policy as expressed in the Act and will be governed by the final adjudication of such issue.

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SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, the registrant certifies it has reasonable grounds to believe it meets all requirements for filing on Form S-3 and has duly caused this Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of Chicago, State of Illinois, on September 10, 2004.

		CLICK COMMERCE, INC.
		By:	/s/ MICHAEL W. NELSON Michael W. Nelson Vice President, Chief Financial Officer and Treasurer

KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Michael W. Nelson and Justin C. Dearborn and each of them (each with full power to act alone), his or her true and lawful attorneys-in-fact and grants, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to sign any and all amendments to this Registration Statement and any related registration statement filed pursuant to Rule 462(b) under the same, with all exhibits thereto, and other documents in connection therewith with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them full power and authority to do and to perform each and every act and thing requisite and necessary to be done in and about the premises, as full and to all intents and purposes as he or she might or would do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents or any of them, or their or his or her substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Act of 1933, this Registration Statement has been signed on September 10, 2004, by the following persons in the capacities indicated.

Name and Signatures		Title

/s/ MICHAEL W. FERRO, JR. Michael W. Ferro, Jr.		Chief Executive Officer and Chairman of the Board (Principal Executive Officer)
/s/ MICHAEL W. NELSON Michael W. Nelson		Vice, President, Chief Financial Officer and Treasurer (Principal Financial and Accounting Officer)
/s/ WILLIAM J. DEVERS, JR. William J. Devers, Jr.		Director
/s/ JUNE E. DREWRY June E. Drewry		Director

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/s/ EMMANUEL A. KAMPOURIS Emmanuel A. Kampouris		Director
/s/ ANDREW J. MCKENNA Andrew J. McKenna		Director
/s/ JOHN F. SANDNER John F. Sandner		Director
/s/ SAMUEL K. SKINNER Samuel K. Skinner		Director
/s/ NEELE E. STEARNS, JR. Neele E. Stearns, Jr.		Director

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IMPORTANT NOTICE TO READERS
TABLE OF CONTENTS
CLICK COMMERCE, INC.
RISK FACTORS
FORWARD-LOOKING STATEMENTS
USE OF PROCEEDS
DIVIDEND POLICY
DESCRIPTION OF CAPITAL STOCK
MATERIAL U.S. FEDERAL TAX CONSIDERATIONS FOR NON-U.S. HOLDERS
SELLING STOCKHOLDERS
PLAN OF DISTRIBUTION
WHERE YOU CAN FIND MORE INFORMATION
INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE
LEGAL MATTERS
EXPERTS
PART II INFORMATION NOT REQUIRED IN THIS PROSPECTUS
SIGNATURES