Japanese encephalitis is a severe central nervous system (CNS) disease with a high case fatality rate in humans. We characterized T-cells infiltrating the brain after infection with Japanese encephalitis virus (JEV) in a mouse model and determined the clonality of the infiltrating T-cells by analyzing the sequences of complementary determining region 3 (CDR3) of the T-cell receptor. C3H/He mice died after intraperitoneal infection with the JaTH160 strain of JEV, demonstrating CNS degeneration and prominent T-cell infiltration. The percentages of T-cells bearing the VA5-1, VA17-1, VA19-1, VB2-1, VB8-3 and VB13-1 subfamilies were significantly increased following infiltration of the brains in infected mice. Additionally, CDR3 size spectratyping revealed the oligoclonality in T-cells bearing VA11-1 and VA18-1. CDR3 amino acid sequences were then determined for the VA5-1, VA11-1, VA18-1, VB8-3 and VB13-1 subfamilies. There were high levels of identity and similarity in amino acid sequences of CDR3 in these T-cells. Quantitative real-time PCR analysis also revealed that CD8, interferon-gamma and tumor necrosis factor-alpha were highly expressed in the infected mouse brain. These results indicate that T-cells with high clonality and similarity infiltrate the JEV-infected mouse brain, and that these T-cells are mainly CD8-positive and have the Th1/Tc1 phenotype.