Multiple sclerosis (MS) and neuromyelitis optica (NMO) are presumed to be an autoimmune disease in the central nervous system (CNS). Although lipids are most abundant components in the nervous system, it has been believed that cellular and/or humoral immunity to various myelin proteins causes these neuroinflammatory diseases. Recent research advances enable us to study lipids in the membranes and some key molecules involved in various neurological disorders including Guillain-Barré syndrome, Alzheimer's disease, Parkinson's disease, and prion disease, are localized in lipid rafts. In MS and NMO, the key molecules for the pathogenesis or the target molecules for the treatments of MS and NMO are also localized in lipid rafts. Here in this article, we highlight on the possible involvement of lipid rafts in the pathogenesis and treatment of MS and NMO and introduce our recent observation of aquaporin 4 regarding NMO.