Ovarian cancer is one of the primary causes of death for women all through the Western world. Baicalin and baicalein are naturally occurring flavonoids that are found in the roots and leaves of some Chinese medicinal plants and are thought to have antioxidant activity and possible anti-angiogenic, anti-cancer, anxiolytic, anti-inflammatory and neuroprotective activities. Two kinds of ovarian cancer (OVCAR-3 and CP-70) cell lines and a normal ovarian cell line (IOSE-364) were selected to be investigated in the inhibitory effect of baicalin and baicalein on cancer cells. Largely, baicalin and baicalein inhibited ovarian cancer cell viability in both ovarian cancer cell lines with LD50 values in the range of 45-55 mu M for baicalin and 25-40 mu M for baicalein. On the other hand, both compounds had fewer inhibitory effects on normal ovarian cells viability with LD50 values of 177 mu M for baicalin and 68 mu M for baicalein. Baicalin decreased expression of VEGF (20 mu M), cMyc (80 mu M), and NFkB (20 mu M); baicalein decreased expression of VEGF (10 mu M), HIF-1 alpha (20 mu M), cMyc (20 mu M), and NFkB (40 mu M). Therefore baicalein is more effective in inhibiting cancer cell viability and expression of VEGF, HIF-1 alpha, cMyc, and NF kappa B in both ovarian cancer cell lines. It seems that baicalein inhibited cancer cell viability through the inhibition of cancer promoting genes expression including VEGF, HIF-1 alpha, cMyc, and NF kappa B. Overall, this study showed that baicalein and baicalin significantly inhibited the viability of ovarian cancer cells, while generally exerting less of an effect on normal cells. They have potential for chemoprevention and treatment of ovarian cancers.