Using reverse transcription-polymerase chain reaction with primers derived from well-conserved genomic areas among all four hepatitis E virus (HEV) genotypes (I-W), the HEV sequence was identified in serum samples obtained from 3 (3%) out of 95 60- to 90-day-old pigs in Japan and characterized molecularly. In the partial sequence of open reading frame (ORF) 2 of 421 nucleotides, the three swine isolates (swJ570, swJ681, and swJ791) showed the highest similarity of 83-87% to genotype III HEV representing human and swine strains (US1, US2, and swUS1) in the United States. The full-length nucleotide sequence of swJ570 consisted of 7225 nucleotides excluding the poly(A) tail and contained ORF 1 encoding 1703 amino acids (aa), ORF2 encoding 660 aa, and ORF3 encoding 122 aa. The swJ570 strain was most closely related to a Japanese strain (JRA1), which had been obtained from a hepatitis patient who had not traveled outside Japan. The overall nucleotide sequence identity between them was 89% and the deduced amino acid sequence identities of ORFI, ORF2, and ORF3 were 96, 99, and 98%, respectively. These results indicate that a certain proportion of pigs in Japan are HEV-viremic and may act as reservoirs of HEV infection, and that the presence of an indigenous strain(s) of HEV should be taken into consideration for the diagnosis of acute hepatitis in Japan.