Cytochrome P450 2A13 (CYP2A13) is a human CYP enzyme that is selectively expressed in the respiratory tract. It plays an active role in the metabolic activation of a tobacco-specific procarcinogen. In this study, the entire coding sequence and the exon-intron junctions of the CYP2A13 gene obtained from 395 Japanese individuals were screened for genetic polymorphisms. Eight genetic polymorphisms were found, of which seven gave rise to known variant alleles: CYP2A13*2, CYP2A13*3, CYP2A13*4, CYP2A13*6, and CYP2A13*7. We identified a novel single nucleotide polymorphism (SNP), 5792T>C, in exon 7 that caused an amino acid substitution (Ile331Thr). One of the 395 individuals included in the study was heterozygous for the variant allele, and therefore, the frequency of the allele in the study population was 0.13%.