Over the last few years, various autoantibodies against cell surface or intracellular antigens were identified in association with several forms of encephalitis, i.e. autoimmune encephalitis. Immunoprecipitaion and sequence analysis of the target protein (proteomics) provided the identification of the antigens corresponding to autoantibodies in autoimmune encephalitis. Appropriate preparation of antigens (synthesized peptides, or recombinant proteins prepared in E.coli or cultured mammalian cells) and assay systems (immunoblot, ELISA, immunoprecipitation or cell-based assay) should be selected for detection of each autoantibodies.Limbic encephalitis characterized by psychosis, dementia, seizures and abnormal movements is a common form of autoimmune encephalitis. Autoantibodies against the NMDA receptor, the AMPA receptor or the VGKC complex (LGI1 and Caspr2) were identified in limbic encephalitis with or without tumor association. Especially, limbic encephalitis associated with anti-NMDA receptor and ovarian teratoma became a distinct neurologic disorder to date.The intracellular antigens are also involved in several forms of encephalitis. Cerebellar ataxia is a common form of autoimmune encephalitis (cerebellits). The autoimmune cerebellar ataxia consists of paraneoplastic ataxia (anti-Yo etc.), anti-GAD-autoantibodies associated ataxia, gluten ataxia (anti-gliadin) and ataxic form of Hashimoto's encephalitis (anti-NAE).The early and accurate diagnosis of autoimmune encephalitis is important because most patients show responses to immunotherapy.