The incidence of prostate cancer is much lower in Asian than Western populations. Environmental factors, such as dietary habits, may play a major role in the causation of prostate cancer. Although isoflavones have been suggested to show a preventive effect against prostate cancer in animal experiments, the results of epidemiologic studies are inconsistent. Here, we conducted a population-based prospective study in 43,509 Japanese men ages 45 to 74 years who generally have a high intake of isoflavones and low incidence of prostate cancer. Participants responded to a validated questionnaire, which included 147 food items. During follow-up from 1995 through 2004, 307 men were newly diagnosed with prostate cancer, of which 74 cases were advanced, 220 cases were organ localized, and 13 cases were of an undetermined stage. Intakes of genistein, daidzein, miso soup, and soy food were not associated with total prostate cancer. However, these four items decreased the risk of localized prostate cancer. In contrast, positive associations were seen between isoflavones and advanced prostate cancer. These results were strengthened when analysis was confined to men ages >60 years, in whom isoflavones and soy food were associated with a dose-dependent decrease in the risk of localized cancer, with relative risks for men in the highest quartile of genistein, daidzein, and soy food consumption compared with the lowest of 0.52 [95% confidence interval (95% CI), 0.30-0.90], 0.50 (95% CI, 0.28-0.88), and 0.52 (95% CI, 0.29-0.90), respectively. In conclusion, we found that isoflavone intake was associated with a decreased risk of localized prostate cancer.