The plant flavonol fisetin is a common dietary component that has a variety of established biological effects, one of which is the inhibition of the enzyme DNA topoisomerase II (topo II). Compounds that inhibit topo II can exert genotoxic effects such as DNA double strand breaks, which can lead to the induction of kinetochore- or CREST-negative micronuclei. Despite reports that fisetin is an effective topoisomerase II inhibitor, its genotoxic effects have not yet been well characterized. Genotoxicity testing of fisetin was conducted in TK6 and HL60 cell lines and the cells were analyzed for malsegregating chromosomes as well as for the induction of micronuclei. Using the cytokinesis-blocked CREST micronucleus assay to discriminate between micronuclei formed from chromosomal breakage (CREST-negative) and chromosomal loss (CREST-positive), a statistically significant increase in CREST-positive micronuclei was seen for all doses tested in both cell lines. CREST-negative micronuclei, however, were significantly increased at the higher test concentrations in the TK6 cell line. These data indicate that at low concentrations fisetin is primarily exerting its genotoxic effects through chromosomal loss and that the induction of DNA breaks is a secondary effect occurring at higher doses. To confirm these results, the ability of fisetin to inhibit human topoisomerase II-alpha was verified in an isolated enzyme system as was its ability to interfere with chromosome segregation during the anaphase and telophase periods of the cell cycle. Fisetin was confirmed to be an effective topo II inhibitor. In addition, significant increases in the number of mis-segregating chromosomes were observed in fisetin-treated cells from both cell lines. We conclude that fisetin is an aneugen at low concentrations capable of interfering with proper chromosomal segregation and that it is also an effective topo II inhibitor, which exerts clastogenic effects at higher concentrations.