Beyond the known mutagenic properties of DNA lesions, recent evidence indicates that several forms of genomic damage dramatically influence the catalytic activities of DNA topoisomerases. Apurinic sites, apyrimidinic sites, base mismatches, and ultraviolet photoproducts all enhance topoisomerase I-mediated DNA cleavage when they are located in close proximity to the point of scission. Furthermore, when located between the points of scission of a topoisomerase II cleavage site, these same lesions (with the exception of ultraviolet photoproducts) greatly stimulate the cleavage activity of the type II enzyme. Thus, as found for anticancer drugs, lesions have the capacity to convert topoisomerases from essential cellular enzymes to potent DNA toxins. These findings raise exciting new questions regarding the mechanism of anticancer drugs, the physiological functions of topoisomerases, and the processing of DNA damage in the cell.