To investigate nationwide the prevalence of hepatitis E virus (HEV) infection in the general population of Japan, serum samples were collected from 22,027 individuals (9,686 males and 12,341 females; age, mean +/- standard deviation: 56.8 +/- 16.7 years; range: 20-108 years) who lived in 30 prefectures located in Hokkaido, mainland Honshu, Shikoku, and Kyushu of Japan and underwent health check-ups during 2002-2007, and were tested for the presence of IgG, IgM, and IgA classes of antibodies to HEV (anti-HEV) by in-house ELISA and HEV RNA by nested RT-PCR. Overall, 1,167 individuals (5.3%) were positive for anti-HEV IgG, including 753 males (7.8%) and 414 females (3.4%), the difference being statistically significant (P < 0.0001). The prevalence of anti-HEV IgG generally increased with age and was significantly higher among individuals aged >or=50 years than among those aged <50 years (6.6% vs. 2.7%, P < 0.0001). Although 13 individuals with anti-HEV IgG also had anti-HEV IgM and/or anti-HEV IgA, none of them had detectable HEV RNA. The presence of HEV RNA was further tested in 50 or 49-sample minipools of sera from the remaining 22,014 individuals, and three individuals without anti-HEV antibodies tested positive for HEV RNA. The HEV isolates obtained from the three viremic individuals segregated into genotype 3 and were closest to Japan-indigenous HEV strains. When stratified by geographic region, the prevalence of anti-HEV IgG as well as the prevalence of HEV RNA or anti-HEV IgM and/or anti-HEV IgA was significantly higher in northern Japan than in southern Japan (6.7% vs. 3.2%, P < 0.0001; 0.11% vs. 0.01%, P = 0.0056; respectively).