Inclusion body myositis (IBM) is an autoimmune, inflammatory myopathy where morphological changes of muscle, including ragged red fibers, have indicated mitochondrial dysfunction in some muscle fibers. In this study enzyme histochemical analysis showed that cytochrome c oxidase (COX)-deficient muscle fibers were present at a frequency ranging from 0.5 to 5% of the muscle fibers in a series of 20 IBM patients. In age-matched controls, only occasional COX-deficient muscle fibers were present. Polymerase chain reaction (PCR) analysis of DNA extracted from muscle tissue of the IBM patients showed multiple mtDNA deletions. PCR analysis of isolated, single muscle fibers showed presence of mtDNA with only one type of deletion and deficiency of wild-type mtDNA in each COX-deficient muscle fiber. This finding was supported by results from in situ hybridization using different mtDNA probes on consecutive sections. A 5 kb deletion was identified in all 20 IBM patients. DNA sequencing of the breakpoint region showed that this deletion was the so-called "common deletion." Most but not all of the investigated deletion breakpoints were flanked by direct repeats. COX-deficient fibers were more frequent among fibers with positive immunostaining with antibodies directed toward a regeneration marker, the Leu-19 antigen, than in the entire fiber population. These results show that COX deficiency in muscle fiber segments in IBM is associated with deletions of mtDNA. Clonal expansion of mtDNA with deletions may take place in regenerating muscle fibers following segmental necrosis.