A diagnostic control methodology provides reduced disruption of device operation when performing diagnostics on devices within a computer system. A diagnostic application notifies a device driver that controls a particular device that diagnostics should be performed during a period of low activity on the device. In response to receiving the notification, the device driver waits for a time of low activity and either notifies the application to unload the device driver and load a diagnostic device driver, or enters a diagnostic mode directly if such operation is supported by the functional device driver. A timeout duration can be specified, and may be set by the notification, so that the diagnostics will be performed within the timeout period even if a time of low activity has not occurred by the expiration of the timeout.