Stem cells are traditionally classified as being either embryonic stem cells (ESCs) or somatic stem cells. Such a designation has now become blurred by the advent of ostensibly pluripotent cells derived from somatic cells, referred to as induced pluripotent stem cells. Mitochondria are the membrane bound organelles that provide the majority of a cell's chemical energy via their production of adenosine triphosphate. Mitochondria are also known to be vital components in many cell processes including differentiation and apoptosis. We are still remarkably uninformed of how mitochondrial function affects stem cell behavior. Reviewed evidence suggests that mitochondrial function and integrity affect stem cell viability, proliferative and differential potential, and lifespan. Mitochondrial status therefore has profound and as yet unexamined implications for the current drive to develop induced pluripotent stem cells as a therapeutic resource.