The purpose of this study was to investigate the prevalence of hepatitis E virus (HEV) infection in swine and humans in different environments in Java and Bali, Indonesia. The prevalence of anti-HEV antibodies in people over 20 years old living in communities in Bali was significantly higher than that in Java. While 68.8% and 90.0% of swine in Bali were anti-HEV positive at 1 and 2 months of age, respectively, swine in Java were at significantly lower risk of HEV infection by the age of 2 months. Our present data suggest that substantial differences in swine-breeding conditions and human living environments affect the rate of HEV infection in humans and swine.