Abstract: A computer system and method is disclosed that aids a user in automatically generating patient documentation. Users, such as physicians, can access the system over a network. Upon a user navigating a flow chart to diagnose and/or manage a patient's condition, textual or other documentation of the path taken through the flow chart is automatically generated. Actions in the same or other systems can also be performed automatically based on the path taken through the flow chart, such as launching a scheduling system for scheduling a patient follow-up visit, automatically placing an order for a test, automatically scheduling a task on to a medical worker's task list, automatically generating a referral letter, or automatically generating patient educational material from a template, as a few examples. If an action on the flow chart requires additional information, a separate window can be opened to allow the user to enter the additional information.