Current research on the mitochondrial permeability transition pore (PTP) and its role in cell death faces a paradox. Initially considered as an in vitro artifact of little pathophysiological relevance, in recent years the PTP has received considerable attention as a potential mechanism for the execution of cell death. The recent successful use of PTP desensitizers in several disease paradigms leaves little doubt about its relevance in pathophysiology; and emerging findings that link the PTP to key cellular signalling pathways are increasing the interest on the pore as a pharmacological target. Yet, recent genetic data have challenged popular views on the molecular nature of the PTP, and called into question many early conclusions about its structure. Here we review basic concepts about PTP structure, function and regulation within the framework of intracellular death signalling, and its role in disease pathogenesis.