Mitochondria play an essential role in the health and development of eukaryotic organisms. They possess many levels of quality control to maintain their proper functioning. The first level is protein quality control (PQC), which is maintained by a vast network of chaperones and proteases, that assist in the proper folding of newly imported or synthesised proteins, the refolding of denatured proteins and the removal of irreversibly damaged or unassembled proteins. The major PQC components within the mammalian mitochondrial matrix include chaperones mtHsp60/10, mtHsp70, TRAP-1 and proteases m-AAA, LONM and CLPXP. The substrates of LONM and CLPXP are not well characterised and the mechanisms by which substrate proteins are recognised are unknown. Currently it remains unclear if LONM and CLPXP degrade different substrates or if there is cooperation between these proteases for the complete clearance of the same substrate. Current research into the substrate specificity of LONM and CLPXP will be reported.