The plant alkaloid berberine has many biological activities including the ability to induce cell cycle arrest and apoptosis, making it a potentially useful agent for targeting cancer cells. We have analyzed the effects of berberine on MCF-7 breast cancer cells. Berberine was added to MCF-7 cells in culture, and proliferation, side population (SP) cells and expression of ABCG2 were examined. Berberine caused a dose-dependent reduction in proliferation. Hoechst 33,342 dye staining and FACS analysis revealed that berberine treatment caused a decrease in SP cells relative to untreated controls. In addition, berberine treatment was associated with a decrease in expression of ABCG2 relative to untreated controls. These results indicate that the growth inhibitory effects of berberine treatment on MCF-7 cells may be partly via effects on SP and ABCG2 expression. Further work is warranted to explore whether berberine may be a novel therapeutic drug useful for targeting breast cancer stem cells.