Mitochondria are cell organelles in charge of ATP production, regulation of intracellular Ca2+ concentration and reactive oxygen species and they have an important role in the intrinsic pathway for activation of apoptotic mechanisms. Mitochondria play a key role in all cells, including stem cells. The development of stem cell biology has long neglected the effects of mitochondria on stem cells, and only recent studies have investigated the influence of mitochondria on potency, proliferation and the degree of differentiation of stem cells. In order to monitor the mitochondrial influence on stem cells, it is important to visualize the mitochondria themselves. The aim of this study was to visualize mitochondria in human oral mucosa stem cells and mouse neural stem cells using the commercial dye MitoTracker. The influence of normoxic and hypoxic conditions on the shape and amount of mitochondria in mouse neural stem cells was observed. One group of stem cells was in normoxia until they underwent fixation. Another group of cells spent 24 hours in hypoxia. After that, one of the subgroups spent 6 hours and another one 24 hours in normoxia until they were fixated. Using MitoTracker® Red CMXRos, we succeeded in visualizing and defining the shape of mitochondria in both stem cell populations. We have found that, under normoxic conditions, the mitochondrial dynamics of neural stem cell does not change, whereas if the neural stem cells are first put under hypoxic and then under normoxic conditions, their mitochondrial dynamics does change.