Inhibition of the nucleotide excision repair (NER) proces is believed to cause the potentiation of the genotoxic and mutagenic effects of DNA damaging agents like UV-light or cisplation by metal ions. However, the precise underlying molecular mechanism of this phenomenon is still unknown. Using in vitro assays, we have determined the potential interference of several metal (II) ions with the lesion recognition and strand incision/displacement steps of the NER mechanism, independently from the DNA polymerization step. When combinations of an optimal Mg2+ concentration and concentrations of various metal ions in a range from 0.1 to 1 mM were tested, all combinations, with Mn2+ and Ni2+ expected, inhibited specifically the incision repair activity by human protein extracts. There was a good correlation for Cd2+, Co2+, Fe2+, Fe2+, Hg2+, Pb2+ and Zn2+ between an inhibiting effect on the incision activity and a reduced protein binding activity to a damaged DNA probe as assessed by gel mobility shift assay.