The aim of this study was to clarify the mechanisms of apoptosis, cytotoxicity, DNA damage and fragmentation, as well as the production of reactive oxygen species (ROS) and Ca+2, induced by berberine in human promyelocytic leukemia HL-60 and murine myelomonocytic leukemia WEHI-3 cells. The levels of Bcl-2 and Bax, the changes of mitochondria membrane potential (MMP), cytochrome c release and activation of caspase-3 were also investigated in both cell lines. The flow cytometry and DAPI staining assays indicated that berberine induced cytotoxicity in both cell lines examined. Flow cytometry assay also showed that berberine induced ROS and Ca+2 production, decreased the levels of MMP and increased the activity of caspase-3 in both cell lines examined. Berberine-induced apoptosis was accompanied by increased levels of Ca+2 and a decrease in the mitochondrial membrane potential, leading to the release of cytochrome c and the cleavage of pro-caspase-3. Western blotting also showed that berberine increased the levels of Bax and cytochrome c and decreased the levels of Bcl-2 in both cell lines. Inhibition of caspase-3 activation (z-VAD-fmk: cell-permeable broad-spectrum caspase inhibitor) completely blocked berberine-induced apoptosis in both HL-60 and WEHI-3 cells. Therefore, berberine induced apoptosis in both examined cell lines through the activation of caspase-3.