The relationship of the intake of soy products and the incidence of colon cancer was prospectively evaluated in a population-based cohort study in Japan. The total intake of soy products and isoflavones in a daily diet was estimated from a validated questionnaire administered at the baseline. The participation rate of the questionnaire was 92.0%. The participants were followed from 1992 to 2000, and colon cancer diagnoses were identified at the main hospitals in the study area. In the analysis, 13,894 men and 16,327 women were included. The medians for energy-adjusted soy product intake were 85.52 g/day for men and 79.60 g/day for women. During follow-up, 111 men and 102 women were diagnosed with colon cancer. A Cox-proportional hazard model was applied to assess the risk of colon cancer incidence. Among women, the risk was reduced with an increased soy product consumption; the hazard ratio in the highest tertile was 0.56 (95% CI 0.34-0.92) compared as the lowest tertile (trend: P=0.04), after adjusting for multiple potential confounders. Among men, no significant association was observed. Our results exhibited the weak benefit of soy foods only among women. Further research to confirm our results may be beneficial.