The nucleotide sequences at the extreme 5' and 3' ends of swine hepatitis E virus (swine HEV) genome were determined, and genomic sequence of swine HEV is now complete. Sequence analysis revealed that the 3' and 5' non-coding regions (NCRs) of swine HEV are closely related to that of the US-1 and US-2 strains of human HEV. Like the two U.S. strains of human HEV, an extra G residue immediately proceeding the poly(A) tail was identified in swine HEV. The 5' NCR of swine HEV also differed from many HEV strains: it lacks an A residue at its 5' very end, and the extra 9 nucleotides in the US-2 strain. In the 3' NCR, swine HEV shared 90-91% nucleotide sequence identities with the US-1 and US-2 strains but only about 58-65% identities with other HEV strains. This study further suggests that the US-1 and US-2 strains of human HEV may be of swine origin. The availability of the complete sequence of swine HEV should facilitate the construction of an infectious cDNA clone of swine HEV.