OBJECTIVE: This study investigated cytotoxicity and induction of apoptosis in human cervical cancer cells (HELA) and prostate cancer cells (PC-3) using the most active fraction of Moringa peregrina seed extract. METHODS: Dried and powdered seeds were extracted using 95% ethanol. The total ethanolic extract was further dissolved in distilled water and separated into petroleum ether, chloroform, ethyl acetate and aqueous extracts. Based on the results of in vitro anticancer studies of all extracts, the most highly active extract was selected for evaluation of apoptosis induction and cell cycle analysis on HELA and PC-3 cells at its half maximal inhibitory concentration using flow cytometry; DNA fragmentation by agarose gel electrophoresis and the expression of protein were measured by Western blot. RESULTS: The chloroform fraction from the ethanolic extract of M. peregrina (CFEE) was the most active antitumor fraction. The selectivity index, determined using the normal Vero cell line, indicated that CFEE had a high degree of selectivity against HELA and PC-3 cells. CFEE induced apoptosis, confirmed by cell cycle arrest at sub-G phase and DNA fragmentation. CFEE induced an increase in mRNA expression of caspase-3, a decrease in Bcl-2 mRNA expression, and decreased ATP levels. CFEE increased protein expression of caspase-3 and decreased protein expression of poly-ADP-ribose polymerase-1 (PARP-1). Flow cytometric analysis showed an appreciable increase in the number of cells in the early apoptotic stage in CFEE-treated HELA and PC-3 cells. CFEE treatment significantly increased lipid peroxidation (malondialdehyde level) in HELA and PC-3 cells. CONCLUSION Seed extract of M. peregrina displayed a significant antitumor effect through apoptosis induction in HELA and PC-3 cells.