The risks of anal and vulvar cancer are strongly related to cigarette smoking. Smokers are exposed to a substantial quantity of tobacco-specific nitrosamines, including 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). NNK is present in the mucus of the female genital tract. The enzyme debrisoquine 4-hydroxylase (CYP2D6) activates NNK and is present in foreskin kerotinocytes and cervical epithelial cells. A polymorphism for the gene CYP2D6 exists, and persons who possess alleles that are associated with reduced levels of CYP2D6 activity might be expected to be at a relatively lower risk of cancers arising from NNK exposure. To test this hypothesis, we conducted a case-control study to examine the association of CYP2D6 genotype and the incidence of anal and vulvar cancer among cigarette smokers in western Washington State. We tested for 14 alleles (*1-*12, *14, and *17) among cases (25 men and 43 women with anal cancer, 64 women with vulvar cancer) and controls (30 men and 110 women). Contrary to the hypothesis, cases were not less likely than controls to have one (43.9 versus 40.7%) or two (6.8 versus 4.3%) inactivating alleles (*3, *4, *5, *6, *7, *8, *11, or *12). There was a suggestion that, if anything, the combined anal and vulvar cancer risk increased (rather than decreased) with an increasing number of CYP2D6 inactivation alleles: odds ratio = 1.2, 95% confidence interval = 0.7-2.0 with one inactivating allele; odds ratio = 1.8, 95% confidence interval = 0.6-5.4 with two inactivating alleles. These results provide no support for the hypothesis that cigarette smokers who carry the CYP2D6 alleles that result in a low activity phenotype have a decreased risk of anogenital cancer.