Since about 60 years a phenomenon now called permeability transition is known in mitochondria. It involves a large pore in the inner mitochondrial membrane, the permeability transition pore (PTP) whose molecular structure is still unknown. Year after year, new hypotheses have been developed how this pore could look like and which proteins cold be structural elements. Enormous progress was made in understanding function, rich pharmacology, and possible biochemical modulation of the PTP. However, many of the structural hypotheses that seemed to be well established by experiments had to be rejected later after their falsification by further experiments. The aim of this review is to give a brief insight into confirmed and less known details of the nature of the pore and of its function. Thereafter, this review will critically report about some of the unknown elements and hypotheses that had to be rejected. © 2013 IUBMB Life, 65(3):255–262, 2013.