We exposed simian virus 40-infected CV-1 monkey cells to the carcinogen N-acetoxy-acetylaminofluorene and monitored the removal of lesions from cellular DNA and from various regions of viral DNA. Exposure to 5.5 microM 3H-labeled carcinogen produced 20-80 adducts per 10(6) bases in cellular DNA in different experiments. The initial adduct concentration in viral DNA was always approximately half that in cellular DNA. At various times after treatment, cellular and viral DNA, and restriction fragments of viral DNA, were purified and examined for adduct density. Independent of the initial adduct concentration three rates of repair were observed. Cellular DNA was repaired at the lowest rate. Viral DNA was repaired about 50% more rapidly than was cellular DNA isolated from the same carcinogen-treated monolayers. Within the viral DNA a 366-base pair region containing the major nuclease-hypersensitive site was repaired at twice the rate of the rest of the viral genome. This region contains regulatory sequences that govern the initiation of DNA replication and viral gene expression. As reported previously this region was initially modified 1.71 +/- 0.20-fold higher than expected from its guanine content. Selective repair diminished the extent of hypermodification of this region by 6.0 +/- 2.1% per hour, partly compensating for the higher initial level of adducts.