Embodiments described herein provide methods for treating various conditions and diseases using an optical signal. In one or more embodiments an apparatus is providing having an optical window, which is used to deliver an optical signal to provide stimulation to one or more tissue sites in the body such as the brain, optic nerve, eye, ganglia, spine, or other like site. The optical signals can be used to treat a variety of neurological diseases and conditions including epilepsy, migraine headaches and chronic pain. In particular applications the optical signals can be used to treat, inhibit or prevent epileptic or other neurological seizures by providing an optical input to a foci or surrounding tissue in the brain causing the seizure. The optical signal may also be combined with an electrical signal to produce an aggregate effect in tissue for treating the disease or condition such as a neurological disease or condition.