Abstract Objective To investigate the association between several types of soy products and all cause and cause specific mortality. Design Population based cohort study. Setting Japan Public Health Centre-based Prospective Study, which includes 11 public health centre areas in Japan. Participants 92 915 participants (42 750 men and 50 165 women) aged 45 to 74 years. Exposures Intake of total soy products, fermented soy products (natto and miso), non-fermented soy products, and tofu from a five year survey questionnaire. Main outcome measures All cause and cause specific mortality (cancer, total cardiovascular disease, heart disease, cerebrovascular disease, respiratory disease, and injury) obtained from residential registries and death certificates. Results During 14.8 years of follow-up, 13 303 deaths were identified. In the multivariable adjusted models, intake of total soy products was not significantly associated with total mortality. Compared with the lowest fifth of total soy product intake, the hazard ratios in the highest fifth were 0.98 (95% confidence interval 0.91 to 1.06, P _trend =0.43) in men and 0.98 (0.89 to 1.08, P _trend =0.46) in women. Intake of fermented soy products was inversely associated with all cause mortality in both sexes (highest versus lowest fifth: 0.90 (0.83 to 0.97), P _trend =0.05 in men, and 0.89 (0.80 to 0.98), P _trend =0.01 in women). Natto showed significant and inverse associations with total cardiovascular disease related mortality in both sexes. Conclusions In this study a higher intake of fermented soy was associated with a lower risk of mortality. A significant association between intake of total soy products and all cause mortality was not, however, observed. The findings should be interpreted with caution because the significant association of fermented soy products might be attenuated by unadjusted residual confounding.