Monascus-fermented red rice has traditionally been used as a natural food colorant or food preservative of meat and fish for centuries. Recently, it has become a popular dietary supplement due to many of its bioactive constituents being discovered. Commercial Monascus-fermented red rice was used in this study. According to the cell-based cytotoxicity assay, a compound with selective cytotoxicity was found and identified as ankaflavin. Ankaflavin was found to be toxic to human cancer cell lines Hep G2 and A549 with a similar IC50 value of 15 microg/mL, while it posed no significant toxicity to normal MRC-5 and WI-38 cells at the same concentration. For elucidating the possible mode of cell death, Hep G2 cells were treated with ankaflavin for 48 h to examine the morphological change of the chromatin. Chromosomal condensation and fragmentation were found, and a significant sub-G1 peak was found by flow cytometry. Apoptosis was therefore suggested as the possible mechanism. Monascin, an analogue of ankaflavin, was also tested in this study. However, it showed no cytotoxicity and did not induce death of Hep G2 cells.