Levels of several cytokines were evaluated in the sera of patients with neuromyelitis optica (NMO) and paraneoplastic or nonparaneoplastic autoimmune encephalitis (AE) and healthy controls (HC). AE patients had higher serum interleukin-17 (IL-17), interferon-gamma (IFN-γ), and IL-12 levels than NMO patients and HC. Also, AE patients with antibodies to cell surface antigens (voltage-gated potassium channel, N-methyl-d-aspartate receptor) displayed increased serum Th17 cytokine (IL-17, IL-23) levels as compared with AE patients with antibodies to intracellular antigens (Hu, Yo), NMO patients, and HC. Aquaporin-4 (Aqp-4) antibody positive NMO patients had higher serum IL-9 levels than Aqp-4 antibody negative NMO patients. IL-17, IL-23, IL-12, and antibody levels were significantly correlated in AE patients with antibodies to cell surface antigens. Our results support the notion that different pathogenic mechanisms are involved in central nervous system diseases associated with antibodies to intracellular and cell surface neuronal antigens. T helper 1 (Th1)-/Th17-type immunities and IL-9 might be important therapeutic targets in AE and NMO, respectively.