Apoptosis may be viewed as a triphasic process. During the pre-mitochondrial initiation phase, very different pro-apoptotic signal transduction or damage pathways can be activated. These pathways then converge on the mitochondrion, where they cause the permeabilization of the inner and/or outer membranes with consequent release of soluble intermembrane proteins into the cytosol. The process of mitochondrial membrane permeabilization would constitute the decision/effector phase of the apoptotic process. During the post-mitochondrial degradation phase downstream caspases and nucleases are activated and the cell acquires an apoptotic morphology. Recently, a number of different second messengers (calcium, ceramide derivatives, nitric oxide, reactive oxygen species) and pro-apoptotic proteins (Bax, Bak, Bid, and caspases) have been found to directly compromise the barrier function of mitochondrial membranes, when added to isolated mitochondria. The effects of several among these agents are mediated at least in part via the permeability transition pore complex (PTPC), a composite channel in which members of the Bcl-2 family interact with sessile transmembrane proteins such as the adenine nucleotide translocator. These findings suggest that the PTPC may constitute a pharmacological target for chemotherapy and cytoprotection.