To compare the epidemiologic profiles of hepatitis A virus (HAV) and hepatitis E virus (HEV) infections in children in Mongolia, the prevalence of HAV and HEV infections was studied serologically and molecularly among 520 apparently healthy children 7-12 years of age (mean +/- standard deviation, 8.5 +/- 0.8 years) using serum samples obtained in 2004. Total antibody against HAV (anti-HAV) was detected in 438 children (84.2%), whereas IgG antibody against HEV (anti-HEV IgG) was detected in only three subjects (0.6%). All three subjects with anti-HEV IgG were negative for anti-HEV IgM and HEV RNA. The presence of HAV RNA was tested in all 520 subjects, and one child (9-year-old girl) was found to have detectable HAV RNA (subgenotype IA). In conclusion, HEV infection was uncommon, but subclinical HAV infection was highly prevalent among children in Mongolia.