An extract of Alnus japonica (Betulaceae) cortex has been traditionally used for purifying blood, and curing feces containing blood, enteritis, diarrhea, alcoholism and cut wounds. In the present study, we demonstrated that the ethanol extract of Alnus japonica (EAJ) exhibited significantly cytotoxicity in human colon adenocarcinoma HT-29 cells. The results showed that the induction of apoptosis in HT-29 cells by EAJ was characterized by chromatin condensation and activation of caspase-3. EAJ-induced activation of caspase-9 and -3 caused the cleavage of poly ADP-ribose polymerase (PARP) and the release of cytochrome c. The expressions of Bcl-2 and Bid were reduced by EAJ in HT-29 cells, whereas pro-apoptotic protein Bak was increased in the cells. EAJ-induced, dose-dependent induction of apoptosis was accompanied by sustained phosphorylation of MAP kinases (JNK and p38 MAPK), ASK1, and p53. NAC administration, a scavenger of ROS, reversed EAJ-induced cell death. In conclusion, these results indicated that EAJ can cause apoptosis through a ROS-mitochondria-caspases-dependent pathway in human HT-29 cells.