Deletions of the mitochondrial genome were identified in 21 out of 58 patients (36 percent) with mitochondrial myopathies, 47 of whom had defects in the mitochondrial respiratory chain. In cases with Complex I defects, the deleted regions of mtDNA, were confined to structural genes encoding Complex I subunits but additionally involved the intervening tRNA genes and in one case included the large and small rRNA genes. In cases with more extensive loss of respiratory chain function, the deletions eliminated genes encoding subunits of Complexes I, IV and V, as well as several tRNAs. Complex I and Complex IV polypeptides were usually normal in deleted cases. This was in contrast to 7 out of 22 patients without detectable mtDNA deletions, who showed specific deficiencies of subunits encoded by nuclear genes. Further studies in one of these cases pointed to defective translocation of the Rieske precursor from the cytosol into the mitochondria. The genetic basis of the disease in 15 cases without detectable deletions or specific subunit deficiencies, remains unknown. The multiple biochemical abnormalities encountered in these cases would be consistent with more subtle alterations of the mitochondrial genome.