In the muscle biopsy of a female patient with chronic progressive external ophthalmoplegia (CPEO), myopathy, and exercise intolerance, the heteroplasmic deletion of a single nucleotide (DeltaT5885) in the mitochondrial tRNA tyrosine gene (tRNA(Tyr)) was found. The mutation was associated with the mitochondrial phenotype of individual muscle fibers, suggesting a causal association of DeltaT5885 with the mitochondrial disease phenotype. The microdeletion was absent from the patient's and her relatives' blood, indicating a spontaneous somatic origin.