Mn2+ is sequestered by liver and brain mitochondria via the mitochondrial Ca2+ uniporter. The mitochondrial Ca2+ uniporter is a cooperative transport mechanism possessing an external activation site and a transport site. Ca2+ binding to the activation site greatly increases the velocity of uptake of both Ca2+ and Mn2+. Electron paramagnetic resonance (EPR) shows that over 97% of the Mn2+ in the mitochondrial matrix is normally bound to the membrane or to matrix proteins. EPR measurements of manganese within living isolated mitochondria can be repeated for hours, and during this time most of the manganese remains in the Mn2+ state. Mn2+ is transported out of mitochondria via the very slow Na(+)-independent efflux mechanism, which is an active (energy-requiring) mechanism. Mn2+ is not significantly transported over the Na(+)-dependent efflux mechanism, which is the dominant efflux mechanism in heart and brain mitochondria. Mn2+ inhibits the efflux of Ca2+ through both of these efflux mechanisms, having an apparent Ki of 7.9 nmol/mg protein on the Na(+)-independent efflux mechanism and an apparent Ki of 5.1 nmol/mg on the Na(+)-dependent efflux mechanism. Mn2+ inhibition of Ca2+ efflux may increase the probability of the mitochondria undergoing the mitochondrial permeability transition (MPT). Intramitochondrial Mn2+ also inhibits State 3 mitochondrial respiration using either succinate or malate plus glutamate as substrate. The data suggest that Mn2+ depletes cellular energy supplies by interfering with oxidative phosphorylation at the level of the F1ATPase and at much higher concentrations, at Complex I. Effects such as these could lead to apoptosis in active neurons.