The operating system routes all keystrokes and mouse input to the system message queue, converting these input events into messages, and posts them, one at a time, to the proper application-defined message queues. An application retrieves messages from its queue and dispatches them to the appropriate window procedures, which process the messages.

Mouse and keyboard input events in the system message queue are strictly ordered so that a new event cannot be processed until all previous events are fully processed: the system cannot determine the destination window of an input event until then. For example, if a user types a command in one window, clicks the mouse to activate another window, then types a command in the second window, the destination of the second command depends on how the application handles the mouse click. The second command would go to the second window only if that window became active as a result of the mouse click.

It is important for an application to process all messages quickly to avoid slowing user interaction with the system. A message must be responded to immediately in the current thread, but the processing it initiates should be done asynchronously in another thread that has no windows in the desktop tree.

The OS/2 operating system can display multiple windows belonging to several applications at the same time. To manage input among these windows, the system uses the concepts of window activation and keyboard focus.