Mitochondria are complex organelles whose internal structure and cytosolic organization is controlled by a growing number of 'mitochondria-shaping' proteins. These include mitochondrial proteins such as the large dynamin-related GTPases Mitofusin (Mfn) 1 and 2, Optic Atrophy 1 (Opa1); as well as the cytosolic dynamin-related protein 1 (Drp1) and its receptor on the outer mitochondrial membrane Fis1. These proteins influence not only the shape of mitochondria, but also the function of the organelle and eventually integrated cellular signalling cascades, including apoptosis. We undertook a genetic approach to elucidate the function and regulation of these proteins. Opa1 is involved in the regulation of mitochondrial fusion, by co-operating with Mfn1. Moreover, Opa1 independently from mitochondrial fusion regulates the crista remodelling pathway of apoptosis. Oligomers of a membrane bound and a soluble form of Opa1, produced by Parl, an inner membrane rhomboid protease, are disrupted early during apoptosis, leading to remodelling of the mitochondrial cristae and redistribution of the mitochondrial cytochrome c. The importance of this pathway is substantiated by the phenotype of the Parl-/- mouse, which displays excess apoptosis in multiple tissues. Cells lacking Parl are more susceptible to apoptotic stimuli and the reintroduction of a soluble form of Opa1 rescues their phenotype.