BACKGROUND The anticarcinogenic and antiatherogenic properties of soy have been demonstrated in experimental studies. To evaluate the relationship between soy product intake and mortality from several types of cancer and heart disease, an ecological analysis was performed in 47 prefectures in Japan. METHODS Age-standardized mortality rates for heart disease and stomach, colorectal, lung, breast and prostate cancer were obtained from the National Vital Statistics, 1995. Information on major nutrient and soy product intake was obtained from the National Nutritional Survey Report 1980-1985. In this survey, dietary habits were surveyed annually by 3-day diet record in about 6000 randomly selected households. RESULTS Soy protein intake was significantly correlated with stomach cancer mortality rate in men after controlling for total energy, alcohol and salt intake, and the mean age and proportion of current smokers in the prefecture (r = -0.31, P = 0.04). Soy product intake estimated as total amount as well as isoflavone and soy protein intake were significantly positively correlated with colorectal cancer mortality rates in both sexes (for total amount, r = 0.32, P = 0.03 in men and r = 0.44, P = 0.001 in women) after controlling for covariates. The inverse correlation between soy product intake (as total amount or soy protein) and heart disease mortality rate was statistically significant in women after controlling for covariates (r = 0.32, P = 0.04 and r = -0.31, P = 0.045, respectively). CONCLUSIONS The present study provides modest support for the preventive role of soy against stomach cancer and heart disease death.