Abstract Numerous effective anticancer drugs have been developed from botanical sources. Although the anticancer properties of Scutellaria baicalensis extract (SbE) have been reported, in some of our studies, SbE did not inhibit the growth of breast cancer cells significantly. In certain concentrations, it increased cancer cell growth. To identify the active anticancer constituents in SbE, we isolated a baicalin-knockout fraction (SbF1) and a baicalin-fraction (SbF3). We evaluated the anti-breast cancer activities of the fractions and their constituents on human breast cancer MCF-7 cells. Using a Waters 2960 high performance liquid chromatography (HPLC) instrument and a Phenomenex Prodigy ODS(2) column, we determined the contents in the extract and fractions: scutellarin, baicalin, baicalein and wogonin. The antiproliferative effects were assayed using the modified trichrome stain (MTS) method. The active properties of the fraction/constituents on the cancer cell cycle and on apoptosis were evaluated using a BD FACScan flow cytometer. A one-way ANOVA was used to measure statistical significance. HPLC data showed that the content of scutellarin, baicalin, baicalein and wogonin in SbE were 0.03, 15.67, 5.19 and 1.42%, respectively. The major constituents of SbF1 are the aglycons, baicalein (40.54%) and wogonin (12.35%). SbF3 contains only the glycoside baicalin (16.68%). SbF1 showed a significant antiproliferative effect. Treatment with 100 g/ml of SbF1 for 72 h inhibited MCF-7 cell growth by 81.6% (P<0.01); at the same treatment concentration, SbF3 increased cell growth by 22.6% (P<0.01). Therefore, SbF1 is the active fraction of SbE. Compared to control (48% of G1-phase, 33% of M-phase, and 10% of G2/M-phase), after treatment with 50 g/mL of SbF1 for 72 h, 27% of cells were in G-phase, 41% of cells were in M-phase, and 23% of cells were in G2/M-phase. SbF1 increased the S- and G2/M-phases in MCF-7 cells. After treatment for 48 h, the percentage of early apoptotic cells induced by 50 g/mL of SbF1 was 12.4%; by 100 g/mL, the percentage was 24.2%. SbF1 significantly increased induction of cell apoptosis compared to control, 6.7%. Studying the effects of four flavonoids in SbE, two glycosides (scutellarin and baicalin) and two aglycons (baicalein and wogonin), on MCF-7 cell proliferation showed that baicalein and wogonin significantly inhibited MCF-7 cell growth at 10–100 µM. In contrast, at certain concentrations (5–50 µM), the glycosides scutellarin and baicalin increased cancer cell growth. These phytochemical and biological data suggest that the active anticancer constituents in SbE are flavonoid aglycons. Since the two glycosides promoted MCF-7 cells at certain concentrations, these compounds should be removed from the S. baicalensis extract to ensure chemopreventive activities. Citation Information: Cancer Prev Res 2010;3(1 Suppl):A71.