B cells are thought to play a pathogenic role in multiple sclerosis (MS), an autoimmune disease affecting the central nervous system (CNS). This idea is supported by the reduction of disease in MS patients undergoing antibody-mediated B cell depletion therapy. In contrast, in experimental autoimmune encephalomyelitis (EAE), a mouse model of MS, B cells have been shown to play a regulatory role. This is suggestive of a dual role for B cells in CNS autoimmunity. It is possible that a critical balance between the pathogenic and regulatory populations of B cells might be involved in the manifestation of the disease. Although in mice, different B cell subsets have been shown to exert immunoregulation through varied mechanisms, the phenotype of regulatory B cells in humans and factors affecting their function are not well known. Also, the origin and development of regulatory B cells is not known. It is important to thoroughly identify the different populations of B cells that might be involved in suppressing CNS autoimmunity, their mode of function and factors that regulate their immunosuppressive properties for using regulatory B cells as a therapy for MS. Here we present methods to study the phenotype and mechanisms of immune suppression by B cells in different mouse models of EAE.