Relatively little is known regarding the role of mitochondrial metabolism in stem cell biology. Here we demonstrate that mouse embryonic stem cells sorted for low and high resting mitochondrial membrane potential (⌬⌿ m L and ⌬⌿ m H) are indistinguishable morphologically and by the expression of pluripotency markers, whereas markedly differing in metabolic rates. Interestingly, ⌬⌿ m L cells are highly efficient at in vitro mesodermal differentiation yet fail to efficiently form teratomas in vivo, whereas ⌬⌿ m H cells behave in the opposite fashion. We further demonstrate that ⌬⌿ m reflects the degree of overall mammalian target of rapamycin (mTOR) activation and that the mTOR inhibitor rapamycin reduces metabolic rate, augments differentiation, and inhibits tumor formation of the mouse embryonic stem cells with a high metabolic rate. Taken together, our results suggest a coupling between intrinsic metabolic parameters and stem cell fate that might form a basis for novel enrichment strategies and therapeutic options.Stem cells persist throughout the entire life span of the organism, suggesting that these cells may possess unique abilities to deal with issues such as oxidative stress and DNA damage. Such supposition is supported by experimental evidence that murine embryonic stem cells (mES) 4 cells appear resistant to exogenous oxidative stress (1). This resistance has been attributed to increased antioxidant protein defenses in mES cells when compared with more differentiated mouse cells (1). There is also evidence that stem cells may preferentially reside in low oxygen niches (2). The best studied example appears to be for hematopoietic stem cells where both theoretical and direct experimental evidence suggests that hematopoietic stem cells preferentially reside within the most hypoxic regions of the bone marrow (3, 4). It has long been known that lowering ambient oxygen concentrations can regulate mitochondrial metabolism and hence alter intracellular reactive oxygen species generation (5). In this context, it is believed that residing within low oxygen environments may help reduce the long term exposure of the stem cell to oxidative damage.Consistent with a role for ambient oxygen in determining stem cell fate, a number of reports have previously demonstrated that low levels of oxygen might promote hematopoietic stem cell function (6 -8). Similarly, it has been demonstrated that the differentiation of mES cells into hematopoietic progenitors was augmented under hypoxic conditions (9). Such observations are not, however, limited to hematopoietic differentiation as oxygen concentration appears to also affect the differentiation of neural stem cells (10, 11), as well as placental cytotrophoblast cells (12).The precise molecular bases for these effects are unclear. Several studies have implicated that activation of hypoxia-inducible factor 1␣ (HIF-1␣) or HIF-2␣ may play a significant role in the observed enhanced differentiation of stem cells under low oxygen conditions (2). Such observations are supported by st...