Human microsomal and soluble epoxide hydrolases (mEH and sEH) are enzymes that metabolize xenobiotic molecules. We screened DNA from 48 Japanese individuals for single-nucleotide polymorphisms (SNPs) in both genes by direct sequencing of the entire genomic regions containing EPHX1 and EPHX2, except for repetitive elements. This approach identified 33 SNPs in the EPHX1 gene; 6 of them were located in the 5' flanking region, 17 in introns, 8 in exons, and 2 in the 3' flanking region. In the EPHX2 gene, we identified 36 SNPs, including 4 in the 5' flanking region, 24 in introns, 5 in exons, and 3 in the 3' flanking region, as well as one insertion/deletion polymorphism in the 5' flanking region. These variants may contribute to a more precise understanding of the nature of correlations between genotypes and disease-susceptibility phenotypes that have been postulated in regard to human microsomal and soluble epoxide hydrolases.