Mitochondria have their own genome, which is essential for proper oxidative phosphorylation and hence for a large part of ATP production in a cell. Although mitochondrial DNA-less (rho(0)) cells can survive under certain conditions, the integrity of the mitochondrial genome is critical for the survival of multicellular organisms. Mitochondrial DNA (mtDNA) is damaged more than nuclear DNA because mitochondria produce a large amount of reactive oxygen species and tend to accumulate toxic xenobiotics. Therefore, there is keen interest in mechanisms that maintain the integrity of mtDNA. DNA repair may play an important role. The repair of mtDNA has been investigated less intensely than nuclear DNA repair because, for a long time, it was thought that mitochondria lacked DNA repair systems. In fact, DNA damage can be repaired in mitochondria. Base-excision repair in mitochondria is well established. The enzymes responsible for mtDNA repair have been identified and are encoded by the same genes as their nuclear counterparts. Mitochondrion-targeting sequences are generated through alternative splicing of mRNAs, alternative use of transcription initiation sites, or alternative use of translation initiation sites. In addition to DNA repair, the degradation of damaged mtDNA may be tolerated because there are multiple copies of mtDNA molecules in a cell.