The Gampaha Deputy Provincial Director of Health Services (DPDHS) division reported a large number of Japanese encephalitis (JE) cases during 1996 to 1997. Notified cases included unconfirmed and confirmed cases. A study to determine the true disease burden was considered necessary. The proportion of undifferentiated fever cases due to Japanese encephalitis virus (JEV) varies in different populations and the Sri Lankan situation is not known. The objectives were to determine the proportion of undifferentiated fever cases and encephalitis cases due to JEV and the case fatality rate and frequency of neurological sequelae in JE in a tertiary care hospital in Gampaha. A cross-sectional descriptive study was carried out in the paediatric and medicine units of the North Colombo Teaching Hospital, Ragamafrom 1998 to 2000. Ninety three randomly selected patients with a diagnosis of undifferentiated fever from whom paired sera could be collected and 32 patients suspected of encephalitis which were not overtly due to mumps, measles or chicken-pox were included. The Armed Forces Research Institute in Medical Sciences Enzyme linked immunosorbent assay for anti-JEV immunoglobulin M and G was used to confirm JEV infection. One of 93 (1.08%) undifferentiated fever cases was due to JEV infection. Eleven of 32 (34.38%) encephalitis cases had JEV infection and 3 (27.3%) had IgM antibodies to JEV in cerebrospinal fluid. Case fatality rate and sequelae at discharge were 11.1% each. JEV was an important cause of encephalitis in Gampaha during this period.