Although it is generally known that mitochondria are defective in DNA damage processing, little is known about the DNA repair pathways and mechanisms that exist in these vital organelles. Certain lesions that are removed by base excision repair are efficiently removed in mitochondria, whereas some bulky lesions that are removed by nucleotide excision repair are not repaired in these organelles. There has been much interest in whether mitochondria possess activities for recombination repair, and some previous studies have reported such activities, whereas others have not. We have taken the approach of studying the formation and removal of interstrand cross-links (ICLs) in DNA. These lesions are thought to be repaired by a repair mechanism that involves nucleotide excision and recombinational repair. The formation and repair of DNA ICLs by 4'-hydroxymethyl-4,5',8-trimethylpsoralen was investigated in both the nuclear and mitochondrial genomes in hamster cells. Seven-fold-higher levels of ICLs were generated in mtDNA than in the dihydrofolate reductase gene, clearly indicating that the mitochondrial genome is a preferential target of 4'-hydroxymethyl-4,5',8-trimethylpsoralen damage. ICLs were removed efficiently from the dihydrofolate reductase gene, but no repair was observed in mtDNA. Our observations support previous work showing efficient gene-specific repair of these lesions in the nucleus but suggest that repair of this type of ICL does not exist in the mitochondria. The preferential damage of mtDNA and the absence of cross-link repair further suggests that mtDNA may be a biologically important target for psoralen.