Physiological stimuli causing an increase of cytosolic free Ca²⁺ [Ca²⁺]_c or the release of Ca²⁺ from the endoplasmic reticulum invariably induce mitochondrial Ca²⁺ uptake, with a rise of mitochondrial matrix free [Ca²⁺] ([Ca²⁺]_m). The [Ca²⁺]_m rise occurs despite the low affinity of the mitochondrial Ca²⁺ uptake systems measured in vitro and the often limited amplitude of the cytoplasmic [Ca²⁺]_c increases. The [Ca²⁺]_m increase is typically in the 0.2–3 μM range, which allows the activation of Ca²⁺-regulated enzymes of the Krebs cycle; and it rapidly returns to the resting level if the [Ca²⁺]_c rise recedes due to activation of mitochondrial efflux mechanisms and matrix Ca²⁺ buffering. Mitochondria thus accumulate Ca²⁺ and efficiently control the spatial and temporal shape of cellular Ca²⁺ signals, yet this situation exposes them to the hazards of Ca²⁺ overload. Indeed, mitochondrial Ca²⁺, which is so important for metabolic regulation, can become a death factor by inducing opening of the permeability transition pore (PTP), a high conductance inner membrane channel. Persistent PTP opening is followed by depolarization with Ca²⁺ release, cessation of oxidative phosphorylation, matrix swelling with inner membrane remodeling and eventually outer membrane rupture with release of cytochrome c and other apoptogenic proteins. Understanding the mechanisms through which the Ca²⁺ signal can be shifted from a physiological signal into a pathological effector is an unresolved problem of modern pathophysiology that holds great promise for disease treatment