Beyond their fundamental role in energy metabolism, mitochondria perform a great variety of other important cellular functions. However, the interplay among these various roles of mitochondria is still poorly understood, and the underlying mechanisms can be related to system level properties. Importantly, mitochondria localized in different regions of a cell may display different morphology, dissimilar biochemical properties, or may differently interact with other intracellular structures. Recent advances in live imaging techniques have also revealed a functional heterogeneity of mitochondria with respect to mitochondrial redox state, membrane potential, respiratory activity, uncoupling proteins, mitochondrial ROS and calcium. An important and still unresolved question is how the heterogeneity of mitochondrial function and the regional specializations of mitochondria are mechanistically realized in the cell and to what extent this could be dependent on environmental aspects. Distinct mitochondrial subsets may also exhibit different responses to substrates and inhibitors and may vary in their sensitivity to pathology, resistance to apoptosis, oxidative stress, thus also demonstrating heterogeneous behavior. All these observations strongly suggest that the intracellular position, organization and the specific surroundings of mitochondria within the cell define their functional features, while also implying that different mitochondrial subpopulations, clusters or even single mitochondrion may execute diverse processes in a cell. The heterogeneity of mitochondrial function demonstrates an additional level of mitochondrial complexity and is a new, challenging area in mitochondrial research that potentially leads to the integration of mitochondrial bioenergetics and cell physiology with various physiological and pathophysiological implications.