By directly sequencing amplified DNA from 30 patients with non-insulin-dependent diabetes mellitus (NIDDM) who had diabetic family members, we identified a G-to-A mutation at np 3316 in the ND-1 gene of the mitochondrial DNA (mtDNA). DNA from 254 patients with NIDDM or impaired glucose tolerance (IGT), from 154 patients with insulin dependent diabetes mellitus (IDDM) and from 207 non-diabetic control subjects was screened for this substitution. The mutation existed in 5 of 254 Japanese NIDDM or IGT patients (2.0%), but not in other subjects. Its prevalence was significantly higher in NIDDM than in other patients or non-diabetic control subjects. The association of the G-A mutation at np 3316 with glucose intolerance suggests the importance of this area for the development of diabetes.