ObjectiveThe clinical characteristics, treatment and prognosis of children with autoimmune encephalitis in two Chinese tertiary pediatric neurology centers were analyzed to improve the understanding of the disease. MethodsA retrospective study of children (0~18 years old) with autoimmune encephalitis in two Chinese tertiary pediatric neurology centers were analyzed and summarized From May 2012 to January 2017. ResultsThere were 103 children with autoimmune encephalitis, eighty-nine cases with anti-NMDAR encephalitis (86.5%), two cases with anti-LGI1 encephalitis (1.9%), one case with anti-CASPR 2 encephalitis (0.9%), and eleven cases with autoantibodies negative encephalitis (10.7%). ①Eighty-nine patients with anti-NMDAR encephalitis were enrolled. The initial symptoms as follows: seizures, mental behavior disorders, language disorders, movement disorders, sleep disorders, paralysis. Sixty-five cases (73.0%) with seizures. Forty cases (61.5%) with cluster attack and twenty-two cases (33.8%) with status epileptics. Seventy-five cases fully recovered (84.3%), five cases epilepsy(5.6%), four cases cognitive dysfunction (4.5%), three cases mental retardation(3.4%), one case ataxia (1.1%), one case died (1.1%). The predictors of poor outcome were status epilepticus, ICU admission, the antibody of NMDAR-IgG more than 1:100 and second-line immunotherapy. ②eleven cases of antibody negative autoimmune encephalitis, four cases (36.4%)of them had sequela. two cases LGI1 encephalitis, a case of anti-CASPR2 encephalitis. Conclusions：Most of the children with anti-NMDAR encephalitis have good prognosis. Anti-LGI1 encephalitis can be only manifested with sleep disorder or seizure, and have good effect on immunotherapy. Compared with other autoimmune encephalitis in this study, the prognosis of autoimmune encephalitis with antibody negative was poor.