The permeability transition pore (PTP) is a channel of the inner mitochondrial membrane that appears to operate at the crossroads of two distinct physiological pathways, i.e., the Ca²⁺ signaling network during the life of the cell, and the effector phase of the apoptotic cascade during Ca²⁺-dependent cell death. Correspondingly, two open conformations of the PTP can also be observed in isolated organelles. A low-conductance state, that allows the diffusion of small ions like Ca²⁺, is pH-operated, promoting spontaneous closure of the channel. A high-conductance state, that allows the unselective diffusion of big molecules, stabilizes the channel in the open conformation, disrupting in turn the mitochondrial structure and causing the release of proapoptotic factors. Our current results indicate that switching from low- to high-conductance state is an irreversible process that is strictly dependent on the saturation of the internal Ca²⁺-binding sites of the PTP. Thus, the high-conductance state of the PTP, which was shown to play a pivotal role in the course of excitotoxic and thapsigargin-induced cell death, might result from a Ca²⁺-dependent conformational shift of the low-conductance state, normally participating in the regulation of cellular Ca²⁺ homeostasis as a pH-operated channel. These observations lead us to propose a simple biophysical model of the transition between Ca²⁺ signaling and Ca²⁺-dependent apoptosis.