Despite the early characterisation of Ca2+ fluxes in isolated mitochondria and the ability of this ion to up-regulate dehydrogenases of the Krebs cycle, the low affinity of the organelle uptake pathways was a long-standing obstacle to the recognition of a physiological role for mitochondrial Ca2+ uptake. This review begins with a historical account of the main results that proved the contrary and provides a brief description of mitochondrial Ca2+ signals. Then, it discusses the characteristics of Ca2+ regulation of mitochondrial function. Finally, it summarizes recent discoveries on structural aspects of mitochondrial reticulum and its connections to signalling partners such as the endoplasmic reticulum or the plasma membrane.