Defects of mitochondrial (mt) DNA cause a diverse group of incurable, progressive diseases that often lead to severe disability and premature death. Most patients with pathogenic mtDNA defects have a mixture of mutant and wild-type mtDNA (heteroplasmy), and the clinical defect is only expressed when the percentage of mutant mtDNA exceeds a critical threshold. Since mtDNA is continually replicating and being turned over, we have proposed an approach to the treatment of these disorders that utilizes sequence-specific antigenomic peptide nucleic acids (PNAs) to hybridize and specifically inhibit the replication of mutant mtDNA under physiological conditions. By allowing the selective propagation of wild-type molecules, it may be possible to correct the cellular biochemical defect and to prevent the progression of disease. This paper summarizes the experimental progress in this area, including the cellular uptake of PNA molecules and their import into mitochondria both in vitro and in cell culture by the addition of a nuclear-encoded mitochondrial targeting sequence. The possibilities of extending this strategy to the treatment of mtDNA deletion disorders are discussed.