In order to study the seroprevalence of hepatitis E virus (HEV) infection among preschool children in Taiwan, a community-based survey was carried out in 54 kindergartens in 10 urban areas, 10 rural areas, and 2 aboriginal areas randomly selected through stratified sampling. Serum specimens of 2,538 preschool children were screened for the HEV antibodies (anti-HEV) by a commercially available third-generation microparticle enzyme immunoassay. The multivariate-adjusted odd ratios (ORm) with their 95% confidence intervals (CI) were estimated through the multiple logistic regression analysis. A total of 86 children were anti-HEV seropositive, giving a prevalence of 3.4%. The prevalence of anti-HEV was 3.9% (19 of 484) among aboriginal children, a significantly increased seroprevalence compared with those among other ethnic groups after multivariate adjustment significantly (ORm= 7.9; 95% CI= 2.6-24.5; P= 0.0003). Female had a higher anti-HEV seroprevalence than the male (ORm= 1.6; 95% CI= 1.0-2.4; P= 0.04), a statistically significantly was found. The seroprevalence of children was lower than their teachers (ORm= 3.5; 95% CI= 1.8-6.8; P= 0.003). There were increasing seropositive rates of HEV antibody with age in aboriginal areas, but decreasing with age in non-aboriginal areas. The poor water supply system, sewage disposal, domestic animals, and environmental hygiene in the aboriginal areas might have played some role in infection with HEV in Taiwan.