In order to evaluate the Japanese encephalitis virus (JEV) vaccination program in rural Taiwan, we conducted a seroepidemiological survey of JEV among rural children 3 to 6 years of age in Taiwan. The children were selected through a systemic sampling following stratification by age of children in 4 selected aboriginal villages and 4 adjacent nonaboriginal villages. The overall vaccine coverage rate for the primary (2 doses) dose was 81.2% (1853/2281) with higher rates (87.7%-87.9%) found among the more recent birth cohort of 3 to 4 years of age. The neutralizing antibody (NT) against JEV was measured with plaque reduction neutralization test (PRNT) using Nakayama strain as the virus. With a positive NT antibody defined as > or = 1:10 dilution of serum yielding more than 50% plaque reduction, the overall JEV NT antibody positive rate among children receiving 3 doses of vaccine was 67%. However, the age-specific positive rates varied significantly with varying ages; the lowest of 47% being among children 4 years of age which was lower than the rates of 68%, 76% and 87% among children of 3, 5 and 6 years of age, respectively. This trend of rising seropositive rates of JEV antibody with increasing age among 4 and 6 years of age was also noted among children who had received no vaccine, suggesting the importance of natural infection among rural Taiwanese children. Despite the high frequency of natural infection, the seropositive rates of JEV antibody still correlated well with the dose of vaccine received, i.e., 67% (1122/1664), 66% (65/97), 33% (4/12) and 40% (19/47) for children receiving 3, 2, 1, and 0 dose of JE vaccines, respectively (P < 0.0001 Chi-square for trend test). When stratified analysis by dose and by type of vaccines was conducted, a significantly higher seropositive rate of JEV NT antibody was noted among children receiving JE vaccine of Beijing type (87%) than children receiving Nakayama type (39%) (p < 0.0001, Chi-square test). Our data indicated that the JEV vaccination, in conjunction with JEV natural infection, has maintained high JEV NT antibody level among rural children of Taiwan.