An A-to-G point mutation at nucleotide pair (np) 3243 (3243 mutation) in mitochondrial DNA (mtDNA) is a well-known pathogenic mutation, which has been found in approximately 80% of patients with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS). It has been reported that the 3243 mutation also occurs in individuals with non-MELAS phenotypes. The reasons for the phenotypic heterogeneity of the 3243 mutation have not been clarified, although it may be closely related with mtDNA heteroplasmy and their differing proportions in different tissues. We examined the proportion of mutant DNA in muscle specimens at the cellular level using single fiber analysis in five patients with the 3243 mutation: three were diagnosed clinically as having MELAS and two had mitochondrial diabetes mellitus (MDM). In both phenotypes, ragged-red fibers (RRF) contained a higher percentage of mutant DNA (average 89.8%) than non-RRF (average 42.4%). On the other hand, the proportion of mutant DNA in non-RRF revealed a wider range than in RRF and the average was higher in MELAS patients (58.5+/-27.3%) than that in MDM patients (26.3+/-27.9%), which correlated with biochemical and morphological mitochondrial abnormalities in muscle. These findings may reflect the underlying mechanisms of tissue specificity in each phenotype.