BACKGROUND Patients with a patent foramen ovale have a high prevalence of migraine with aura (MA). However, whether patients with an atrial septal defect (ASD) have a high prevalence of migraine remains unclear. The present study aimed to determine the prevalence of migraine and its clinical characteristics in patients with ASD. RESULTS Ninety-five patients (age ≥ 20 years) who had undergone percutaneous ASD closure responded to a questionnaire used by neurologists to diagnose migraine either with or without aura. We diagnosed migraine before ASD closure according to the criteria of the International Headache Society. The overall prevalence of migraine seemed to be higher in the present study than in the Japanese general population (24.2% vs. 9.4%, respectively). All patients with MA were female and significantly younger than those without migraine (p < 0.01). CONCLUSIONS Our findings suggested that the susceptibility to the development of MA differs according to sex and age in patients with cardiac shunt.