Several publications have recently suggested that atrial septal defect may be associated with the physiopathology of headache with migraine-type characteristics. We describe four previously asymptomatic paediatric patients with atrial septal defect who underwent percutaneous Amplatzer septal occluder device implantation and who subsequently developed symptoms compatible with migraine headache. The cases had normal echocardiograms after the intervention and a benign course with headache improvement after several weeks or months. There are paediatric patients with atrial septal defect who may dramatically develop migraine symptoms with or without aura following percutaneous correction of their defect. Large paediatric studies are needed to offer accurate prognoses for children and their families. The possibility of using clopidogrel to treat this type of headache is subject to debate.