The pathogenesis of experimental autoimmune encephalomyelitis (EAE) can be efficiently kept under control by specialized subsets of CD4+ T lymphocytes able to negatively regulate the function of T cells with encephalitogenic potential. A number of observations support a role for such suppressor T cells in controlling early phases of disease development at the level of peripheral lymphoid organs but there is also evidence suggesting immunoregulation within the central nervous system (CNS) microenvironment itself. This review evaluates the sites of regulation based on available data from distinct experimental models. We then discuss these aspects with reference to suppressor CD4+ T cells induced through the epicutaneous application of pure CNS antigens that confer long term protection against EAE. Finally, we give an overview of genes recently discovered to be important in regulation of the immune system that may also prove to be key players in the modulation of EAE and MS.