Aims Although dietary saturated fatty acids (SFA) are considered atherogenic, associations between SFAs intake and stroke and coronary heart disease are still debated. We sought to test the hypothesis that SFA intake is associated inversely with risk of stroke and its subtypes and positively with coronary heart disease among Japanese, whose average SFA intake is lower than that of Westerners. Methods and results The Japan Public Health Center-based prospective Study involves two subcohorts: Cohort I, aged 45-64 in 1995 and followed-up through 2009, and Cohort II, aged 45-74 in 1998 and followed-up through 2007. A total of 38 084 men and 43 847 women were included in this report. Hazards ratios for incident total stroke, ischaemic stroke, intraparhenchymal haemorrhage, subarachnoid haemorrhage, myocardial infarction, and sudden cardiac death across quintiles of dietary SFAs were examined. We found inverse associations between SFA intake and total stroke [multivariable hazard ratio (95% confidence interval) for the highest vs. lowest quintiles = 0.77 (0.65-0.93), trend P = 0.002], intraparenchymal haemorrhage [0.61 (0.43-0.86), P for trend = 0.005], and ischaemic stroke [0.84 (0.67-1.06), trend P = 0.08], primarily for deep intraparenchymal haemorrhage [0.67 (0.45-0.99), P for trend = 0.04] and lacunar infarction [0.75 (0.53, 1.07), trend P = 0.02]. We also observed a positive association between SFAs intake and myocardial infarction [1.39 (0.93-2.08), trend P = 0.046] primarily among men. No associations were observed between SFAs intake and incidence of subarachnoid haemorrhage or sudden cardiac death. Conclusions In this Japanese population, SFAs intake was inversely associated with deep intraparenchymal haemorrhage and lacunar infarction and positively associated with myocardial infarction.