Aza-anthracenediones are a new class of anti-cancer drugs, which demonstrate promising in vitro and in vivo activity. Our laboratory has synthesized a variety of structural analogs in which we determined previously that the positioning of the nitrogen within the backbone, as well as sidearm modification, results in dramatic differences in the potency of cytotoxicity. We reported previously that although DNA reactivity appears to be a necessary component for mediating cell death, it is not sufficient for predicting cytotoxicity of the aza-anthracenediones. We have chosen three aza-anthracenediones (BBR 2828, BBR 2778 and BBR 2378) to investigate the importance of DNA strand breaks and/or protein-concealed DNA breaks induced by aza-anthracenediones. We determined in the present study that, while all three drugs cause DNA breaks as determined by alkaline and neutral elution, as well as KCl-SDS precipitation, these breaks do not correlate directly with their potency as cytotoxic compounds. Further, we found significant differences in the types of DNA breaks induced by these drugs. Finally, we report that the persistence of protein-DNA complexes induced by all three drugs was similar and, therefore, cannot account for differences in the potency of cytotoxicity of the aza-anthracenediones. Thus, we postulate that, while the total number of drug-induced protein-concealed DNA breaks is an important indicator of drug toxicity, it is possible that the actual nature of the breaks may differ among the aza-anthracenedione congeners, and it is these differences in the actual proteins present in the DNA breaks that differentiate between aza-anthracenediones.