In contrast to patent foramen ovale that is highly prevalent in the general population, atrial septal defect (ASD) is a rare congenital heart defect. The effect of ASD closure on headache and migraine remains a matter of controversy. The objectives of our study were (1) to determine headache prevalence in consecutive patients with ASD scheduled for percutaneous closure for cardiologic indications, using the International Classification of Headache Disorders and (2) to compare headache characteristics before and after closure of ASD. In this observational case series no a priori power analysis was performed. Twenty-five consecutive patients were prospectively included over 27 months. Median duration of follow-up was 12 months [interquartile range 0]. Prevalence of active headache seemed to be higher compared with the general population: any headaches 88% (95% confidence interval 70-96), migraine without aura 28% (14-48), migraine with aura 16% (6-35). After ASD closure, we observed a slightly lower headache frequency (median frequency 1.0 [2.6] vs 0.3 [1.5] headaches per month; P = .067). In patients with ongoing headaches, a significant decrease in headache intensity (median VAS 7  vs 5 ; P = .036) was reported. Three patients reporting migraine with aura before the intervention noted no migraine with aura attacks at follow-up, 2 of them reported ongoing tension-type headache, 1 migraine without aura. In summary, this prospective observational study confirms the high prevalence of headache, particularly migraine, in ASD patients and suggests a possible small beneficial effect of ASD closure.