The thymus is a primary lymphoid organ that is responsible for T cell development and maturation. Thymic depletion accompanied by apoptosis and altered T cell maturation occurs during several viral infections. Here we show that adult mice intracerebrally infected with Japanese encephalitis virus exhibit severe cell depletion and alterations in the CD4(+) and CD8(+) single as well as CD4(+)CD8(+) double positive cell populations. A 5.6 fold induction of MHC-I but not MHC-II was observed on thymocytes of such mice and was accompanied with a progressive depletion of thymocytes as the disease progressed with 90% of double positives being depleted by 9 days post infection. Staining studies with propidium iodide and Annexin V revealed that the percent thymocytes undergoing apoptosis had increased significantly in animals infected with Japanese encephalitis virus. Although similar changes in MHC-I expression were also observed in newborn pups challenged with Japanese encephalitis virus, qualitative and quantitative differences in thymocyte depletion were observed relative to the adult thymus. These observations may have implications in the ability of the immune system to respond to specific antigens and possible autoimmunity in survivors of Japanese encephalitis infection.