Topoisomerases maintain DNA structure by relieving torsional stress occurring in DNA during transcription, replication and cell division. Topoisomerases are of two main types, causing transient breaks in one (type I) or both (type II) and strands of DNA, and a number of clinical anticancer drugs are thought to act by inhibiting religation of these transient breaks. Topoisomerase II appears to have a close association with the SMC (stable maintenance of chromosomes) family of proteins involved in organisation of the chromatin in a series of loops on the proteinaceous chromosomal scaffold. Inhibition of topoisomerase II function can result in deletions of such loops, probably mediated by reciprocal exchange of topoisomerase subunits. Disruption of topoisomerase I and/or II function during DNA replication results in smaller DNA deletions and other mutations, probably arising from non-homologous recombination. Inhibition of topoisomerase II action during mitosis and meiosis can cause incomplete separation of chromatids and chromosomes, with the consequent production of genomic mutations. Topoisomerase-mediated mutagenicity is important because it can lead not only to drug resistance but also to drug-induced secondary cancers. Mutagenicity of topoisomerase-directed agents has been underestimated in the past, since these drugs are not usually capable of reacting covalently with DNA and usually have low mutagenicity in microbial assays.