Topoisomerase II is an essential enzyme that plays critical roles in many DNA processes, including chromosome segregation. In order to carry out its important physiological functions, topoisomerase II creates and rejoins double-stranded breaks in the genetic material. Thus, while the enzyme is necessary for cell survival, it also has the capacity to fragment the genome. Topoisomerase II-mediated DNA breaks are sequestered within a covalent enzyme-DNA complex. Normally, these “cleavage complexes” are present at low levels and are tolerated by the cell. However, conditions that significantly increase the physiological concentration or life-time of topoisomerase II-DNA cleavage complexes lead to chromosomal translocations and other mutagenic events, and can induce cell death pathways. The potentially lethal aspect of enzyme mechanism has been exploited by a number of highly successful anticancer agents. Since drugs that increase levels of topoisomerase II-DNA cleavage complexes transform the enzyme into a potent cellular toxin, they are referred to as topoisomerase II “poisons” to distinguish them from compounds that inhibit the catalytic activity of the enzyme. Recent evidence indicates that many DNA lesions also act as topoisomerase II poisons. This finding has provided tremendous insight into enzyme and drug action and raises important questions regarding the physiological interactions of topoisomerase II with DNA damage. Since the DNA cleavage and ligation reactions of topoisomerase II are fundamental to its physiological and pharmacological functions, this review will focus on how the enzyme cuts and rejoins the double helix and how these reactions are altered by topoisomerase II poisons.