Using PCR-RFLP analysis, no A2 allele which is related with the frequency of NIDDM in Finland was detected in Japanese patients with NIDDMs and controls. We found out a new microsatellite of CA repeat in the human muscle glycogen synthase (MGS) gene, and the polymorphism of the repeat number detected by the PCR. The allele frequency was not significantly different between NIDDMs and controls. However, the allele frequency in the patients without high total cholesterolemia was significantly different from that of controls, and 19 repeat allele was significantly higher in this group than that in controls. These suggest that the MGS gene or neighboring genes are related with one of the disease genes of diabetes mellitus without high total cholesterolemia.