Mitochondria are unique among intracellular organelles because they contain their own DNA, which can be transcribed and translated to form proteins. Mitochondrial diseases include myopathies and multisystem disorders. The case of a patient showing bilateral ophthalmoplegia with proximal limb weakness, severe dysphagia and short stature, without family history, is described. The analysis of mitochondrial DNA of the patient muscle revealed a deleted form accounting for 65% of the total mitochondrial DNA. The Southern Blot Analysis of mtDNA allows a rather precise localization of deletions giving new insights in the pathogenesis of mitochondrial myopathies and representing a new precious diagnostic tool in these diseases.