Kearns-Sayre syndrome (KSS) and Pearson syndrome (PS) show quite different phenotypes despite the same underlying genetic defect, i.e. a large deletion of one population of mitochondrial (mt) DNA. The main feature of KSS is progressive encephalomyopathy; on the other hand, PS shows fatal hematological problems in early infancy. Through Southern blot analysis of mtDNA of blood cells, deletion has been consistently found in patients with PS but usually undetectable in KSS patients. Therefore, their different clinical phenotypes have been explained by the different tissue distribution of mutant mtDNA. Recently, a few cases were reported which had features of PS in infancy and later developed KSS. These observations suggest that phenotypes may also be modified by the selection process involving mtDNA within different tissues. We found a case of KSS, who initially presented endocrinological dysfunction such as insulin-dependent diabetes mellitus (IDDM) and growth hormone (GH) deficiency, and had not developed external ophthalmoplegia until the age of 17. Although he did not show any symptoms of PS, a marked proportion of mtDNA was deleted not only in muscle but also in blood cells. Analysis of his blood cells showed an unchanged proportion of deleted mtDNA at three estimations within 6 years of the follow-up period. This case provides evidence that deleted mtDNA in blood cells also has a stable replicative capacity and that a large proportion of deleted mtDNA in blood cells may not accompany hematological problems.