Whether the mitochondrial permeability transition pore (PTP), also called mitochondrial megachannel (MMC), originates from the F-ATP synthase is a matter of controversy. This hypothesis is supported both by site-directed mutagenesis of specific residues of F-ATP synthase affecting regulation of the PTP/MMC and by deletion of specific subunits causing dramatic changes in channel conductance. In contrast, human cells lacking an assembled F-ATP synthase apparently display persistence of the PTP. We discuss recent data that shed new light on this controversy, supporting the conclusion that the PTP/MMC originates from a Ca -dependent conformational change in F-ATP synthase allowing its reversible transformation into a high-conductance channel.