Flavonoids exist extensively in the human diet, and a variety of health effects have been ascribed to them. The cytotoxic effects of 23 flavonoids on breast cancer cells (MDA-MB-231 and MCF-7), col-orectal carcinoma cells (LoVo and DLD-l) and prostatic cancer cells (PC3) were investigated. By comparing the cytotoxicity ($EC_{50}$) of selected molecules that differ in only one structure element, we identified several structural properties associated with enhanced cytotoxicity, including the presence of the 2,3-double bond, appropriate hydroxyl numbers, 3-OH, 6-OH and ortho-hydroxylation in ring B. Flavonoids with a 5-OH exhibited lower cytotoxicity than their non-hydroxylated counterparts. Results indicated that 3,6-dihydroxylflavone showed the most potent cytotoxic effect on these cancer cells. The appearance of apoptotic cells with DAPI staining was observed in cancer cells under 3,6-dihydroxylflavone treatment, and the apoptosis analysis by flow cytometry also showed that 3,6-dihydroxylflavone induced apoptotic cell death in these cancer cells. These results revealed the structurally related toxicity of flavonoids on human cancer cells, and indicates that 3,6-dihydroxylflavone is an active compound worthy of development for cancer chemotherapy.