Japanese encephalitis virus (JEV) is a member of mosquito-borne flaviviruses. The core particle of JEV consists of a multiple copies of the capsid protein. In this study, the author demonstrated that the JEV capsid protein was appeared to be localized predominantly both around the perinuclear membrane structures in the cytoplasm of the JEV-infected cells and within the nucleus by using a mouse JEV capsid-specific antiserum. The presence of the capsid protein within the nucleus was also demonstrated by expression of EGFP-capsid fusion protein from a Sindbis virus-derived expression vector in the transfected cells. Amino acid sequence comparison of several flavivirus capsid proteins similar to JEV revealed that the JEV capsid protein contains a nuclear localization motif Thus our result showing that the JEV capsid protein is localized within the nucleus as well as in the cytoplasm provides an important clue fir the role of the capsid protein in JEV replication.