As one type of adult stem cells (ASCs), human dental pulp stem cells (HDPSCs) have several properties, including high proliferation rate, self?renewal capability, and multi?lineage differentiation. However, the apoptotic mechanism underlying the development of dental pulp cells remains unclear. In the present study, a significant increase of apoptosis was observed in HDPSCs from the deciduous teeth compared with that from adult permanent teeth. In addition, the occurrence of cytochrome c expression and mitochondrial?mediated apoptosis pathway activity in HDPSCs were confirmed by quantitative polymerase chain reaction, and western blotting. Although caspase?8 and caspase?9 showed higher expression in deciduous teeth than in adult permanent teeth, only the knockdown of caspase?9 via RNA interference in HDPSC cells exhibited a significant reduction in apoptosis, and caspase?3 expression and activity. All these results revealed that caspase?9 and activated caspase?3 predominantly regulates cell apoptosis in HDPSCs from deciduous teeth.