Scope Genistein (GEN) is known to be genotoxic via targeting topoisomerase-II (TOPII). Oxidative metabolism of GEN is shown to generate hydroxylated metabolites with catecholic structures. The present study focuses on the impact of oxidative metabolism of GEN, exemplified for 3 '-hydroxygenistein (3 '-OH-GEN) and 6-hydroxygenistein (6-OH-GEN), on topoisomerase interference and the resulting genotoxic potential in HT-29 human colon carcinoma cells. Methods and results In a cell-free decatenation assay, 3 '-OH-GEN slightly exceeds the TOPII-inhibiting potential of GEN. In HT-29 cells, its inhibitory action on TOPII does not differ from GEN, but it has greater activity with respect to causing DNA damage (measured by the comet assay), p53 activation (Western blot), apoptosis induction (ELISA), and cytotoxicity (WST-1 assay). This may to some extent be related to a stronger pro-oxidative potential of 3 '-OH-GEN in comparison to GEN, as observed for the highest concentrations (DCF assay). 6-OH-GEN exerts much weaker toxic effects than GEN in cell-based assays, including TOPII poisoning, DNA strand-breaking potential, and ROS generation. This might in part arise from decreased cellular uptake of the metabolite, as measured by HPLC-DAD. Conclusion Oxidative metabolism alters the toxicological potential of GEN. Depending on the site of oxidation, the toxicity of the parent compound is exceeded (3 '-OH-GEN) or attenuated (6-OH-GEN).