Mitochondrial DNA (mtDNA) inheritance and maintenance and function of the respiratory chain are the result of a synergistic action of the nuclear and the mitochondrial genomes. Mutations in either or both genomes can result in a wide range of multisystemic disorders. We have studied a homoplasmic mtDNA mutation in the tRNA(Ile) gene that segregates exclusively with cardiomyopathy in two unrelated families. Cytochrome c oxidase (COX) deficiency was selectively observed only in the heart tissue and in patient's cardiomyocyte cultures and not in any other cell type, indicating that the defect is tissue specific. To understand the pathogenic mechanism of cardiomyopathy associated with a homoplasmic, tissue specific mtDNA mutation, we constructed transnuclear cardiomyocyte cell lines with normal or patient's nucleus and containing wild type or mutant mtDNA. Of the four cell lines analyzed, COX activity was low only in patient's cardiomyocytes illustrating that both the patient's nucleus and mitochondria are essential for expression of the phenotype. In cells with either wild type nucleus or wild type mtDNA, COX activity was normal. From these results it is evident that a tissue specific nuclear modifier gene may interact synergistically with the mtDNA mutation to cause COX deficiency.