In the pluripotent cellular state, characteristic of preimplantation embryos and embryonic stem cells (ESCs), metabolic activity in general, and mitochondrial function in particular, seems to be subdued; increasing upon differentiation, possibly to avoid oxidative stress-mediated damage. A crucial but overlooked aspect of development is related to how mitochondrial differentiation follows somatic differentiation in terms of producing specific cell fates with very distinct metabolic profiles and energy requirements, notably in two of the most sought after cell fates in the field of regenerative medicine, the neuronal and muscular lineages. Finally, recent evidence suggests that, although induced pluripotent stem (iPS) cells obtained from somatic cells show hallmarks of pluripotency from a mitochondrial standpoint, these characteristics are not as pronounced as those shown by ESCs. Thus, incomplete reprograming might also be reflected in terms of iPS mitochondrial status, with possible implications for the derivation of patient-specific cells.