Several hundreds of mitochondrial proteins are nuclear encoded and are synthesised on cytosolic polyribosomes as precursor proteins. Most of these precursors contain an N-terminal extension called presequence which functions as targeting signal and which is cleaved off after import. Despite the fact that there are no sequence similarities and no consensus for the cleavage site in mitochondrial presequences, cleavage of almost all presequences is catalysed by a single, highly specific metalloendopeptidase, called general mitochondrial processing peptidase (MPP). MPP in plants is integrated into the bc 1, complex of the respiratory chain and both subunits, α-MPP and β-MPP, are identical to the core proteins of the complex. Despite the fact that the bc 1 complex in plants is bifunctional, catalysing both electron transport and protein processing, these two functions are distinct. MPP belongs to the Pitrilysin family of peptidases, characterised by a zinc binding motif, HXXEH 74–76E, involved in catalysis. Both the membrane-bound integrated MPP/bc 1 complex of plants and the soluble mammalian MPP recognise similar higher-order structural elements upstream from the cleavage site that are important for processing. The secondary structure with flexibility and stabilising elements, hydrofobicity, charge and length seem to influence the interaction with MPP. The newly imported non-assembled precursor inside mitochondria is degraded by a proteinase that is distinct from MPP or any other previously characterised proteinases, a novel ATP-dependent, membrane-associated serine-type proteinase.