The quantitative relationship between deleted mitochondrial DNA and the clinical course of patients with Kearns-Sayre syndrome is poorly understood. We investigated this point using tissue samples obtained at age 10 years when the patient was diagnosed as Kearns-Sayre syndrome and at age 20 years when he died of disseminated intravascular coagulation. By long polymerase chain reaction, a shortened mitochondrial genome (8.8 kb; normal, 16.6 kb) was detected in the patient. By quantitative competitive polymerase chain reaction, the percentage of deletion-carrying mitochondrial DNA was not increased as expected and did not differ significantly by tissue type or sampling time or correlate with clinical course. Although we could not demonstrate that the amounts of wild-type mitochondrial DNA decreased with accelerating progression, it was emphasized that such a reduction of mitochondrial DNA in various tissues, including those of the central nervous system, could play a significant pathogenetic role, since only wild-type mitochondrial DNA is functional in patients with large-scale deletions of mitochondrial DNA.