Understanding how clinicians are using clinical information systems to assist with their everyday tasks is valuable to the system design and development process. Developers of such systems are interested in monitoring usage in order to make enhancements. System log files are rich resources for gaining knowledge about how the system is being used. We have analyzed the log files of our Web-based clinical information system (WebCIS) to obtain various usage statistics including which WebCIS functions are frequently being used. We have also identified usage patterns, which convey how the user is traversing the system. We present our method and these results as well as describe how the results can be used to customize menus, shortcut lists, and patient reports in WebCIS and similar systems.