The prevalence of migraine headaches (MH) is 12% in the general population and increases to 40% in patients with patent foramen ovale. This study evaluated the prevalence of MH in patients with congenital heart disease (CHD). Of 466 patients contacted from the UCLA Adult Congenital Heart Disease Center, 395 (85%) completed a questionnaire to determine the prevalence of MH. Patients were stratified by diagnosis of right-to-left, left-to-right, or no shunt. A group of 252 sex-matched patients with acquired cardiovascular disease served as controls. The prevalence of MH was 45% in adults with CHD compared to 11% in the controls (p<0.001). Of the 179 patients with MH, 143 (80%) had migraines with aura and 36 (20%) had migraines without aura versus 36% and 64% observed in the controls (p<0.001). The frequency of MH was 52% in the right-to-left shunt group, 44% in the left-to-right, and 38% in the no shunt group (p=NS). In patients with a right-to-left shunt who underwent surgical repair, 47% had complete resolution of MH, whereas 76% experienced >50% reduction in headache days per month. In conclusion, the prevalence of MH in all groups of adults with CHD is 3 to 4 times more than a sex-matched control population, with increasing prevalence of MH in patients with no shunt, left-to-right, and right-to-left shunt. The higher than expected frequency of MH in patients with CHD without an intracardiac shunt, suggests additional mechanisms to explain the significant association with MH.