In order to study the structure-activity relationships in the series of new intercalating polycyclic agents, 1-amino-substituted pyrido[3,4-b]quinoxalines, benzo[f]pyrido[4,3-b]quinoxaline derivatives bearing a dibasic side chain and their benzo[f]pyrido[3,4-b] isomers have been synthesized. Biological evaluation was carried out for topoisomerase I and II inhibition, and for in vitro and in vivo antitumor properties in several models. Results demonstrate that appropriately substituted benzo[f]pyrido[4,3-b]quinoxaline derivatives are inhibitors of topoisomerase I and II, and have significant antitumor properties in various experimental models. In addition, the most active compounds appear to be minimally recognized by tumor cells expressing the multidrug resistance phenotype.