Few studies have associated height with cardiovascular diseases other than myocardial infarction. We conducted a population-based 36-year cohort study of 12,859 men born in 1955 or 1965 whose fitness for military service was assessed by Draft Boards in Northern Denmark. Hospital diagnoses for ischemic heart diseases, atrial fibrillation, stroke, and venous thromboembolism were obtained from the Danish National Patient Registry, covering all Danish hospitals since 1977. Mortality data were obtained from the Danish Civil Registration System. We began follow-up on the 22nd birthday of each subject and continued until occurrence of an outcome, emigration, death, or 31 December 2012, whichever came first. We used Cox regression to compute hazard ratios (HRs) with 95 % confidence intervals (CIs). Compared with short stature, the education-adjusted HR among tall men was 0.67 (95 % CI 0.54-0.84) for ischemic heart disease (similar for myocardial infarction, angina pectoris, and heart failure), 1.60 (95 % CI 1.11-2.33) for atrial fibrillation, 1.05 (95 % CI 0.75-1.46) for stroke, 1.04 (95 % CI 0.67-1.64) for venous thromboembolism, and 0.70 (95 % CI 0.58-0.86) for death. In conclusion, short stature was a risk factor for ischemic heart disease and premature death, but a protective factor for atrial fibrillation. Stature was not substantially associated with stroke or venous thromboembolism.