A variety of stimuli utilize an increase of cytosolic free Ca(2+) concentration as a second messenger to transmit signals, through Ca(2+) release from the endoplasmic reticulum or opening of plasma membrane Ca(2+) channels. Mitochondria contribute to the tight spatiotemporal control of this process by accumulating Ca(2+), thus shaping the return of cytosolic Ca(2+) to resting levels. The rise of mitochondrial matrix free Ca(2+) concentration stimulates oxidative metabolism; yet, in the presence of a variety of sensitizing factors of pathophysiological relevance, the matrix Ca(2+) increase can also lead to opening of the permeability transition pore (PTP), a high conductance inner membrane channel. While transient openings may serve the purpose of providing a fast Ca(2+) release mechanism, persistent PTP opening is followed by deregulated release of matrix Ca(2+), termination of oxidative phosphorylation, matrix swelling with inner membrane unfolding and eventually outer membrane rupture with release of apoptogenic proteins and cell death. Thus, a rise in mitochondrial Ca(2+) can convey both apoptotic and necrotic death signals by inducing opening of the PTP. Understanding the signalling networks that govern changes in mitochondrial free Ca(2+) concentration, their interplay with Ca(2+) signalling in other subcellular compartments, and regulation of PTP has important implications in the fine comprehension of the main biological routines of the cell and in disease pathogenesis.