In July 1999, a single dose of live-attenuated SA 14-14-2 Japanese encephalitis (JE) vaccine was administered to children living in the Bardiya, Banke and Kailali districts of Nepal. In 2004, the original vaccinated population experienced a fifth seasonal exposure to JE. We performed a case-control study comparing the prevalence of the administration of vaccine in patients with JE hospitalized in the Bardiya and Bheri Zonal hospitals and in age-sex matched controls resident in the Bardiya district. Among the 219 village controls, 114 had been vaccinated (52.1%) while only one of 20 JE cases had received live-attenuated JE vaccine. Five years after administration of a single dose, SA 14-14-2 provided a protective efficacy of 96.2% (CI 73.1-99.9%).