We report histochemical, immunocytochemical, biochemical and molecular studies of skeletal muscle from a 23-year-old man with Kearns-Sayre syndrome. Southern blot analysis revealed a 4.7 kb heteroplasmic deletion of the mitochondrial DNA mapping within genes coding for subunits of complexes I, IV and V of the respiratory chain and for tRNA. Cytochrome c oxidase activity was decreased by 30% in isolated muscle mitochondria, without alteration of the Km. Histochemical and immunocytochemical correlation studies for cytochrome c oxidase revealed a lack of activity in 34% of individual muscle fibers including all the typical ragged-red fibers and a low percentage of immunodeficient fibers.