Evidence has accumulated that berberine is able to induce cell cycle arrest and apoptosis in many human cancer cell lines. However, there is no available information on the effects of berberine on human oral squamous cell carcinoma. In this study, the effects of berberine on cell growth, apoptosis and cell cycle regulation in human oral squamous carcinoma HSC-3 cells were examined. Berberine induced dose- and time-dependent irreversible inhibition of cell growth and cellular DNA synthesis. This was also confirmed by phase-contrast microscopy which showed that berberine induced morphological changes in HSC-3 cells. Propidium iodide/annexin V staining for flow cytometric analysis showed that berberine-induced apoptosis correlated with caspase-3 activation. Flow cytometric studies of the cell cycle distribution showed that berberine induced mainly G0/G1-phase arrest. Flow cytometric examinations also showed that berberine induced reactive oxygen species (ROS) and Ca2+ production, as well as the dysfunction of mitochondrial membrane potential (MMP), which were correlated with apoptosis. In conclusion, our data support that berberine initially induces an endoplasmic reticulum stress response based on ROS and Ca2+ production which is followed by dysfunctions of the mitochondria, resulting in apoptosis of these oral cancer HSC-3 cells. Prolonged exposure of the HSC-3 cells to berberine causes increased apoptosis through reduced levels of MMP, release of cytochrome c and activation of caspase-3.