The nervous and immune systems have similar functional characteristics. Both have an intricate network of synaptic connections and an exquisite communication system that enable intercellular signal transduction. Although semaphorins were originally identified as guidance cues in neural development, accumulating evidence indicates that several semaphorins called ‘immune semaphorins’, such as Sema3A, 4A, 4D, 6D and 7A, are critically involved in various phases of the immune response by regulating immune cell–cell contacts or cell migration. In this review, we present recent knowledge on the functions of semaphorins and their receptors in the immune system and their potential roles in the pathogenesis of multiple sclerosis (MS), a representative CNS autoimmune disease, and its animal model, experimental autoimmune encephalomyelitis (EAE).