Systems and methods involve automatic activation, de-activation or modification of therapies or other medical processes based on brain state. A medical system includes a sensor system having one or more sensors configured to sense signals related to the brain state of the patient. A brain state analyzer detects various brain states, including sleep stage and/or brain seizures. A controller uses the brain state detection information to control a medical system configured to perform at least one respiratory or cardiac process. Methods involve sensing signals related to brain state and determining the brain state of a patient based on the sensed signals. At least one respiratory or cardiac medical process is controlled based on the patient's brain state.