Purpose: Aminoflavone (5-amino-2,3-fluorophenyl)-6,8-difluoro-7-methyl-4H-1-benzopyran-4-one; AF; NSC 686288) is a novel anticancer agent with a unique pattern of growth inhibitory activity in the National Cancer Institute (NCI) 60 tumor cell line screen. Phase I clinical trials with AF will begin soon. We previously demonstrated extensive metabolism of AF by cytochrome P450 (CYP) 1A1 and CYP1A2, metabolic activation, formation of irreversible protein and DNA adducts and p53 stabilization in sensitive, but not resistant, human tumor cell lines treated with AF [9]. The present studies focus on the effects of AF on cellular DNA and cellular responses to DNA damage. Methods: Phosphorylation of H2AX in MCF7 cells treated with AF was determined with immunofluorescence. MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4- sulfophenyl)-2H-tetrazolium) assays were used to determine the effect of cotreatment with caffeine or wortmannin, inhibitors of ataxia-telangiectasia-mutated protein (ATM) and ATR (ATM- and rad3-related protein), on the AF IC50 values for MCF7 cells. DNA damage in MCF7 cells treated with AF was determined by alkaline elution. DNA-topoisomerase complex stabilization was ascertained by the ICE (in vitro complex of enzyme) assay. Results: Treatment of sensitive cells with AF resulted in phosphorylation of H2AX, a histone 2A variant that is phosphorylated in response to DNA damage. AF IC50 values for MCF7 cells were lowered by cotreatment with caffeine or wortmannin, further implicating DNA damage in AF cytotoxicity. There was no evidence of DNA–DNA cross-linking in sensitive cells, but protein-associated single-strand breaks were observed after AF treatment. Although this pattern of DNA damage is commonly associated with topoisomerase poisons, there was no evidence for AF-induced stabilization of either topoisomerase I- or II-DNA complexes. Conclusions: These studies further implicate DNA damage in the cytotoxicity of AF and identify biochemical features of that damage including formation of protein-associated single-strand breaks not involving topoisomerase I or II.