We aimed to investigate the effect of soybean products intake on incidence of type 2 diabetes mellitus (T2DM) in a Japanese population. This study included community residents who underwent annual multiphasic health screening examinations, including a standard 75-g oral glucose tolerance test (OGTT). Our investigation included 1,651 (848 men and 803 women) participants aged 30-79 years who had six eligibility criteria at baseline examination between April 2008 and March 2009: (1) a fasting plasma glucose (FPG) < 7.0 mmol/L ; (2) a 2-h postload plasma glucose (2-h PG) < 11.1 mmol/L ; (3) no history of diabetes, cardiovascular and cerebrovascular disease; (4) body mass index (BMI) < 25.0 kg/m²; (5) waist circumference < 90 cm; and (6) not work on the improvement of the lifestyle recently. We assessed the intake of soybean products from a questionnaire. We used the 1999 WHO criteria to define T2DM: a FPG ≥ 7.0 mmol/L and/or a 2-h PG ≥ 11.1 mmol/L. We followed up the 1,651 participants annually until March 2011. Cox proportional hazards regression was used to estimate hazard ratios (HRs) and 95% confidential intervals (CIs) by sex. We adjusted for age, alcohol consumption, smoking, physical activity, intake of meat and fish, BMI, waist circumference, systolic blood pressure, log-transformed triglycerides and HDL-cholesterol. The mean follow-up was 1.8 years (total person-years: 2954) and 208 individuals developed T2DM during that period. Among men, the multivariate-adjusted HR and 95% CIs for incidence of T2DM was 1.62 (1.08-2.44) in men who intake soybean products lower than 100g compared with men who intake soybean products about 100g. Among women, the intake of soybean products was not significantly associated with incidence of T2DM. In conclusion, lower intake of soybean products was associated with the higher risk for incidence of T2DM in Japanese men.