An inverse association between height and risk of cardiovascular disease has been reported, but the evidence is limited for stroke subtypes, in particular in Asian populations. Further, few studies have examined how socioeconomic status in adulthood influence the relationship between height and risk of cardiovascular disease. This study examined the association between height and risks of stroke and coronary heart disease, and whether education level, an indicator of adult socioeconomic status, modify the effect of height on those risks, within a cohort of the Japan Public Health Center-based Prospective Study (JPHC Study). The hazard ratios for the incidence of cardiovascular disease associated with height were calculated by a 16-year follow-up of 15,564 Japanese men and women, aged 40-59. The hazard ratios were adjusted for age, gender, area, education, occupation and cardiovascular risk factors. Height was inversely associated with risks of total stroke, either hemorrhagic or ischemic stroke but not with coronary heart disease. The adjusted hazard ratios (95% confidence interval (CI)) of total stroke, hemorrhagic stroke, and ischemic stroke for a 1 SD height increments were 0.82 (95% CI: 0.74, 0.90), 0.80 (95% CI: 0.70, 0.92), and 0.83 (95% CI: 0.73, 0.95), respectively. No multiplicative interaction was observed between height and education level on stroke risk. Short stature was associated with increased risk of total stroke, either hemorrhagic or ischemic stroke, independent of adult socioeconomic status and cardiovascular risk factors, but not with risk of coronary heart disease in Japanese men and women.