Anaerobic intestinal bacteria produce various organic acids. We identified the concentrations of various organic acids produced by intestinal bacteria needed to kill cultured cells. Nine organic acids and their sodium salts were added to five epithelial cell lines and the cells were examined for cytotoxicity. To assess cytotoxicity, the colorimetric 3-(4,5-dimethyl-2-thiazoyl-2,5-diphenyl tetrazolium bromide (MTT) assay was performed. We calculated the lowest concentration that killed 50% of the cells by the MTT assay. Adherent and floating cells were collected 96 h after incubation for analysis of apoptosis by gel electrophoresis and flow cytometry. The minimum concentrations of the acids and sodium salts of n-butyric, propionic, isovaleric, and succinic acids capable of causing cytotoxicity were lower than the concentrations produced by intestinal bacteria. Apoptosis was found in all cell lines treated with the acids and the sodium salts of n-butyrate, isobutyrate, propionate, isovalerate, and n-valerate. However, no apoptosis was found in cells treated with the acid or sodium salts of formate and lactate. This study showed that acetate, butyrate, propionate, and valerate produced by intestinal bacteria could induce apoptosis at physiological concentrations. This cytotoxicity may contribute to the pathogenesis of colonic ulcers.