Background: Japanese Encephalitis (JE) had high fatality rate and gave permanent sequelae in more than quarter children affected. Since 1975, JE surveillance in animals found that JE infection had spread throughout the Indonesia regions. Bali is endemic for JE infection, with well enhanced surveillance, and recruited as pilot project area for JE vaccination in Indonesia. Objectives: to assess JE incidence and to investigate JE association with the burden of the disease, the length of stay and severe neurological outcome in Bali province. Methods: We applied clinical case definition of acute encephalitis syndrome (AES) and performed laboratory diagnostic criteria using serum IgM capture ELISA. Results: During the surveillance period, 282 cases were met the AES case definition, 50 (17.7%) were positive for JE infection, resulting in an annual incidence of 1.2/100 000 population. As many as 46 (92%) were under 15 years old. One (0.02%) subject died, while 18 (36%) survivors had a permanent disability due to brain atrophy or degeneration. Most subjects were admitted during the rainy season, but cases were reported throughout the year. The median length of illness was 10 days for subjects with non-JE encephalitis, while median length of illness 19 days for subjects with JE.Â The majority (88%) of JE patients were found to live far from a pigsty and mostly living in town. None of them had a history of JE vaccination. Conclusions: The majority of JE cases in Bali was children under 15 years old, and not living in an area near a pigsty. This pattern similar with the previous study, since there is no immunization program available present. Consideration should be given to JE vaccination policy in the near future.