Several antineoplastic agents used in the treatment of hematologic malignancies exert their cytotoxic effects by inhibiting the activity of nuclear DNA topoisomerase (topo) I or II. Mechanisms of drug resistance to topoisomerase inhibitors have been defined at the molecular level from in vitro studies using model cell lines, and include quantitative and qualitative changes in topo I and II. The possible roles of these mechanisms in clinical drug resistance and clinical outcomes for patients with hematologic malignancies are now under investigation. Available data indicate that the blast content of topo II does not correlate with clinical outcome in acute myeloid leukemia (AML), and this may also be true in acute lymphocytic leukemia (ALL). Chronic lymphocytic leukemia (CLL) cells are resistant to topo II inhibitors because they express low levels of topo II. Further studies using sequential biopsy samples and assays of topoisomerase activity should establish the role that changes in topo I and II activity play in the development of drug resistance in hematologic malignancies.