We performed restriction analysis and Southern blotting of the muscle mitochondrial DNA from 34 patients suffering from different myopathies. In 13/21 patients with chronic progressive external ophthalmoplegia the muscle mitochondrial DNA was shown to be heteroplasmic. Further mapping by use of several restriction enzymes yielded large deletions in muscles from 10/13 chronic progressive external ophthalmoplegia patients. Most of the deletions spanned large parts of the mitochondrial genome, leading to loss of mitochondrial genes encoding several subunits of the respiratory chain complexes I (NADH-dehydrogenase), IV (cytochrome c oxidase) and V (ATP-synthetase), as well as of several tRNAs. Comparison of the mapping data with the histochemical and biochemical results did not provide a clear correlation between the location of the mitochondrial genetic defects and the functional deficiencies of the affected respiratory chain complexes. In the majority of patients with chronic progressive external ophthalmoplegia, but without a family history of the disease, restriction analysis reveals large mutations of the mitochondrial genome, while other methods are necessary for the localization of defects in all cases with maternal transmission of the disease. The same holds true for all other kinds of mitochondrial myopathies based on defects within the nuclear DNA or on derangements of the "cross-talk" between the nuclear and the mitochondrial genomes.