Mitochondrial DNA (mtDNA) mutation is associated with a subtype of non-insulin-dependent diabetes mellitus (NIDDM). We identified two homoplasmic mtDNA mutations at the positions of 3394 (T-C) and 3423 (G-T) in a NIDDM patient with clinical features of mitochondrial encephalopathy. The mtDNA 3394T-C mutation changed a conserved tyrosine to a histidine in NADH dehydrogenase subunit 1. The frequency of mtDNA 3994 T-C mutation was determined with Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) in general NIDDM patients and nondiabetic control subjects. The mutation was seen in 4.9% of NIDDM patients and 1.3% of nondiabetic controls. It is indicated that the mtDNA 3394 T-C mutation is associated with NIDDM in Japan.