Nucleotide excision repair and the long-patch mismatch repair systems correct abnormal DNA structures arising from DNA damage and replication errors, respectively. DNA synthesis past a damaged base (translesion replication) often causes misincorporation at the lesion site. In addition, mismatches are hot spots for DNA damage because of increased susceptibility of unpaired bases to chemical modification. We call such a DNA lesion, that is, a base damage superimposed on a mismatch, a compound lesion. To learn about the processing of compound lesions by human cells, synthetic compound lesions containing UV photoproducts or cisplatin 1,2-d(GpG) intrastrand cross-link and mismatch were tested for binding to the human mismatch recognition complex hMutS␣ and for excision by the human excision nuclease. No functional overlap between excision repair and mismatch repair was observed. The presence of a thymine dimer or a cisplatin diadduct in the context of a G-T mismatch reduced the affinity of hMutS␣ for the mismatch. In contrast, the damaged bases in these compound lesions were excised three-to fourfold faster than simple lesions by the human excision nuclease, regardless of the presence of hMutS␣ in the reaction. These results provide a new perspective on how excision repair, a cellular defense system for maintaining genomic integrity, can fix mutations under certain circumstances.Mismatches in DNA resulting from replication errors, and base damage caused by physical (UV light) and chemical (polyaromatic hydrocarbons) agents, are responsible for the majority of human cancers (18). Although certain mismatches and base lesions can be eliminated from DNA by the base excision repair pathway initiated by glycosylases with narrow substrate ranges, in human cells there exists a general mismatch repair system and a general damage repair system of wide substrate range. The mismatch repair system removes the mismatched base as a nucleotide (44), and the excision repair system excises the damaged base(s) in an oligonucleotide (52, 67).The general mismatch repair system (long-patch mismatch repair) corrects all eight single-base mismatches as well as small insertion sequence loops with comparable efficiencies (31, 44). The general nucleotide excision repair (excision repair) system (8) not only is the sole repair pathway for bulky lesions such as thymine dimers (TϽϾT) and cisplatin-guanine adducts but also repairs a wide variety of nonbulky lesions such as O 6 -methylguanine (O 6 -meG) at physiologically relevant rates (52). Thus, it appears that both repair systems recognize many dissimilar non-B DNA forms rather than a specific lesion structure.Given the wide substrate ranges of both systems, it is not unreasonable to expect overlaps between the two substrate spectra, or that one repair system may facilitate the function of the other. Indeed, it has been shown that the excision repair system recognizes mismatches and removes the mismatched base in a manner identical to the removal of damaged bases (27). Since a DNA lesion, by de...