More than one billion years ago, mitochondria were free-living prokaryotic organisms with their own DNA. However, during the evolution, ancestral genes have been transferred from the mitochondrial to the nuclear genome so that mtDNA became dependent on numerous nucleus-encoded factors for its integrity, replication and expression. Mutations in any of these factors may alter the cross-talk between the two genomes and cause Mendelian diseases that affect mtDNA integrity or expression.