Adaptive brain stimulation systems and methods aids in the rehabilitation of patients from traumatic brain injury, coma, movement disorder, or other brain dysfunction. After a direct brain stimulator is implanted in a brain region of a patient, the patient is stimulated according to a set of stimulation parameters. A present state is measured and compared to a reference state by statistical and medically relevant criteria. The subsequent program of stimulation is dependent upon the outcome of the comparison. An adaptive brain stimulation and reinforcement system and method is also described in which a second area of the brain is stimulated when stimulation of the first brain area produces a desired effect, thereby reinforcing the prior response of the brain.