Currently available information on properties and regulation of mitochondrial Ca2+ transporting systems in eukaryotic cells is summarized. We describe in detail kinetic properties and effects of inhibitors and modulators on the energy-dependent Ca2+ uptake through the Ca2+ uniporter, as well as on Na+-dependent and Na+-independent pathways for Ca2+ release in mammalian mitochondria. Special emphasis is placed on Ca2+ transport systems (for ion uptake and release) in mitochondria of higher plants, algae, and yeasts. Potential physiological implications of mitochondrial Ca2+ fluxes (influx and efflux), e.g., regulation of activity of Ca2+-dependent enzymes of the Krebs cycle, maintaining of cellular Ca2+ homeostasis, and engagement in pathophysiological processes, are discussed.