Background: Migraine is a chronic daily headache which interfere a quality of life. The purpose of this research is to obtain the prevalence, risk factors, and comorbidity of migraine. Methods: A cross sectional study involving 4771 subjects in 5 villages in the district of Central Bogor, Bogor City 2011–2012. Data collection was performed using WHO STEPS (interview, measurement, physical examination, and laboratory test). Results: In this study, the migraine prevalence was 22.43%, with significant risk factors were sex, age, and stress (p < 0.05). Comorbidity of migraine was coronary heart diseases (p < 0.05). There was no significant correlation between migraine with marital status, level of education, smoking, hypertension, obesity, total cholesterol, LDL, HDL, trigliseride level, and diabetes mellitus (p > 0.05). Conclusions: Risk factors which have significant association with migraine are sex, age, and stress, whereas coronary heart disease existed as a comorbidity with migraine.