Previous reports showed that methylated CpG sites are primary targets of bulky lesions induced by UV radiation, benzo[a]pyrene (B[a]P), or other environmental genotoxic agents. This study was performed to determine whether the repair of DNA damage formed preferentially at CpG dinucleotides is sensitive to 5-methylcytosine substitutions. Reactivation assays using UV- or B[a]P diol epoxide-damaged shuttle vectors established that human nucleotide excision repair enzymes are able to process fully methylated target DNA molecules. Repair reactions in human cell extracts suggested that 5-methylcytosines modulate local repair efficiency in a seemingly unpredictable manner. In fact, excision of the predominant (+)-trans-anti-B[a]P−dG adduct situated in a mutational hot spot sequence (codon 273 of the p53 gene) was stimulated by CpG methylation. Interestingly, excision activity was increased by a single 5-methylcytosine residue flanking the adduct in the damaged strand, but the same stimulatory effect was also induced by a single 5-methylcytosine residue located opposite the adduct in the undamaged strand. No such stimulation was observed when the (+)-trans-anti-B[a]P−dG lesion was placed in a different site containing a sequence of contiguous guanines, and strong inhibition was detected when a representative of the rare (+)-cis-anti-B[a]P−dG isomer was tested in the same assay. These results raise the possibility that 5-methylcytosines in CpG dinucleotides modulate not only the distribution of bulky DNA lesions but, at least in some cases, also the kinetics of subsequent excision repair reactions. This study confirms that the efficiency of bulky lesion repair is determined by the configuration of base pairs at damaged sites.