To examine the association of plant-based food intakes with CVD and total mortality among Japanese. In the Japan Collaborative Cohort Study for Evaluation of Cancer Risk, 25 206 men and 34 279 women aged 40–79 years, whose fruit, vegetable and bean intakes were assessed by questionnaire at baseline in 1988–90, were followed for 13 years. Deaths from total stroke, stroke subtypes, CHD and total CVD, according to the International Classification for Diseases 10th Revision, were registered. During 756 054 person-years of follow-up, there were 559 deaths from total stroke, 258 from CHD, 1207 from total CVD and 4514 from total mortality for men, and for women, 494, 194, 1036 and 3092, respectively. Fruit intake was inversely associated with mortality from total stroke (the multivariable hazard ratio (HR (95 % CI)) in the highest v. lowest quartiles = 0·67 (0·55, 0·81)), total CVD (HR = 0·75 (0·66, 0·85)) and total mortality (HR = 0·86 (0·80, 0·92)). Vegetable intake was inversely associated with total CVD (HR = 0·88 (0·78, 0·99)). Bean intake was inversely associated with other CVD (HR = 0·79 (0·64, 0·98)), total CVD (HR = 0·84 (0·74, 0·95)) and total mortality (HR = 0·90 (0·84, 0·96)). Further adjustment for other plant-based foods did not alter the association of fruit intake with mortality from total stroke, total CVD and total mortality, but attenuated the associations of vegetables and beans with mortality risk. In conclusion, intakes of plant-based foods, particularly fruit intake, were associated with reduced mortality from CVD and all causes among Japanese men and women.