We investigated the possible association between alleles of a simple tandem repeat DNA polymorphism in the human glycogen synthase gene and non-obese non-insulin-dependent diabetes (NIDDM) in Japanese subjects. Nine alleles (-4G, -3G, -2G, -1G, 0G, 1G, 2G, 3G, and 4G) were identified in the study group of 164 patients with NIDDM and 115 nondiabetic subjects. The overall frequency distribution of the glycogen synthase gene alleles was significantly different between the two groups (p = 0.0316). The 2G allele was found more frequently in patients with NIDDM than in non-diabetic subjects (17.7 % vs 8.7 %, p = 0.0016). These results suggest that the 2G allele could be a genetic marker of NIDDM in Japanese subjects.