Determination of the total mtDNA sequence of a 42 year-old female with chronic progressive external ophthalmoplegia (CPEO) revealed a heteroplasmic G-to-A transition at nt. 5877 in the tRNA-Tyr gene and a homoplasmic T-to-C transition in the tRNA-Gln gene at 4343. The former mutation was located in a highly conserved nucleotide in the DHU loop. This mutation by restriction enzyme analysis using Ddel was observed only in the blood of her two asymptomatic children and her mother. The tRNA-Gln mutation in the T psi C loop was found in a few controls and in all of her maternal relatives. The cybrid clones including tRNA-Tyr mutation showed decreased oxygen utilization and fragility against oxygen stress. This tRNA-Tyr mutation is tightly associated with CPEO.