There has been rapid progress in the understanding of the protective mechanism against infection during the past decade. We reviewed the genetic susceptibility in familial or recurrent encephalitis/encephalopathy and subacute sclerosing panencephalitis (SSPE). Recessive mutation of UNC-93B1 and dominant mutation of TLR3 were associated with herpes simplex encephalitis (HSE). Those mutations impair the dsRNA-induced IFN-alpha/beta and IFN-lambda production and predispose to HSE. Dominant mutation of RANBP2 (encoding a nuclear pore protein) was detected in familial or recurrent patients with acute necrotizing encephalopathy. Polymorphisms of MxA, IL-4, IRF1, TLR3, PD1 and TLR3 are probably associated with the development of SSPE. Identification of causing or predisposing genes would enable the early diagnosis and the establishment of effective protection or treatment.