We aimed to investigate migraine diagnoses in a hospital setting, use of prescription migraine medicine and levels of serotonin in patients with atrial septal defect. Using Danish national registries to identify all patients born before 1994 diagnosed with atrial septal defect between 1959 and 2013, thus including 2277 patients and a gender and age matched comparison cohort of 22756. Plasma serotonin was measured in 136 patients with a small, unclosed, atrial septal defects and 18 controls. Patients with atrial septal defect had an increased risk of receiving a migraine diagnosis (HR 3.4 (95% CI: 2.6–4.6)) and receiving migraine medicine (HR 1.8 (95% CI: 1.2–2.5)). Ten years after closure, 93% of those using migraine medicine pre-closure, were still receiving this. The risk of having very high plasma serotonin levels was increased in patients with atrial septal defect compared with the control group, but there was no difference in the median values between the two groups. Migraine and use of migraine medicine were increased in atrial septal defect patients. The use of medicine was not diminished by closure of the defect. Plasma serotonin was severely elevated in 18% of the patients with atrial septal defect.