African trypanosomiasis continues to pose a challenge for the development of new chemotherapy. Type II topoisomerases, essential enzymes in nucleic acid metabolism, have proven highly suitable as targets for antibacterial and antitumor therapy. Well-characterized topoisomerase II inhibitors affect the cognate nuclear and mitochondrial enzymes in Trypanosoma equiperdum. Inhibition is accompanied by extensive fragmentation and structural alteration in nuclear and mitochondrial DNA. Some clinically important antitrypanosomal drugs bind to DNA (i.e., pentamidine, isometamidium, diminazene). These agents inhibit the mitochondrial, but not nuclear, topoisomerase II of trypanosomes. These studies suggest that type II topoisomerase inhibitors may prove to be effective and safe new antitrypanosomal drugs.