Embryonic stem (ES) cells are derived from the inner cell mass of blastocysts and have a pluripotency to differentiate into a variety of cell types. ES cells have high resistance to environmental stress compared to functional cells, which can undergo apoptosis when stressed. We have investigated whether ES cells have resistance to multiple types of stress or selective stress. Phytosphingosine (PHS) and staurosporine (STS) were used as chemical stressors. PHS induced mitochondria-mediated apoptosis in several cell lines. STS is a protein kinase inhibitor that induces apoptosis even without mitochondrial involvement. PHS treatment damaged 3T3 mouse fibroblasts, but did not damage ES cells. STS damaged ES cells as well as 3T3 mouse fibroblasts at similar doses. Susceptibility to cell damage is correlated with the retention of the mitochondrial membrane potential. PHS treatment could induce DNA fragmentation in differentiated ES cells. Differences in cell-death susceptibility between the undifferentiated and differentiated states showed that the mitochondria-localised anti-apoptotic protein Bcl-2 was highly expressed in undifferentiated ES cells, which gradually decreased during differentiation. These results suggest that undifferentiated mouse ES cells have a high resistance to mitochondria-involved extracellular stress.