The methylation of DNA at CpG dinucleotides by DNA methyltransferases (MTases) is an epigenetic alteration of the genome that plays an important role in the regulation of gene expression in eukaryotes. Abnormalities in the levels of methylation are one of the hallmarks of tumorigenesis. Polycyclic aromatic hydrocarbons such as benzo[a]pyrene are ubiquitous environmental pollutants that are metabolized in vivo to highly genotoxic and tumorigenic diol epoxides (B[a]PDE). The latter reacts with cellular DNA to form covalent adducts that can, if not removed by cellular DNA repair mechanisms, cause mutations and the initiation of tumorigenesis in animal model systems, and probably in humans. The potential impact of such lesions on DNA methylation has received relatively little attention. Utilizing an in vitro biochemical approach, it is shown that BPDE-derived DNA lesions can alter DNA methylation by prokaryotic MTases M.SssI and M.HhaI and mammalian MTase Dnmt3a at CpG and GCGC sites. These effects depend on the conformational properties of the lesions and their positions within the DNA recognition sequence. The results of these studies suggest that B[a]PDE may initiate cancer not only by genotoxic mechanisms, but might also contribute to tumor development by epigenetic effects that involve changes in DNA methylation status.