The association between the intake of non-alcoholic beverages and CVD in Asians is uncertain. The intake of non-alcoholic beverages was estimated in 77 407 participants of the Japan Public Health Centre-based cohort study aged 45–74 years. The Cox regression calculated the hazard ratios (HR) and 95 % CI for incident CVD according to sex-specific quintiles of intake of non-alcoholic beverages. A total of 4578 incident CVD (3751 strokes and 827 CHD) were diagnosed during a 13·6-year median follow-up. The risks of stroke and total CVD were lower for the highest v. lowest intake quintiles of non-alcoholic beverages in men and women: the multivariable HRs (95 % CIs) were 0·82 (0·71, 0·93, Ptrend = 0·005) and 0·86 (0·76, 0·97, Ptrend = 0·02), respectively, in men and were 0·73 (0·63, 0·86, Ptrend = 0·003) and 0·75 (0·65, 0·87, Ptrend = 0·005), respectively, in women. The reduced risk was evident for both ischaemic and haemorrhagic strokes and was mainly attributable to green tea consumption. The intake of non-alcoholic beverages from coffee and other beverages was not associated with the risk of CVD in both men and women. Also, there was no association between the intake of non-alcoholic beverages and the risk of CHD in either sex. In conclusion, the risks of stroke and total CVD were lower with a higher intake of non-alcoholic beverages in Japanese men and women.