ObjectiveTo evaluate factors associated with new‐onset migraine (NOM) after transcatheter atrial septal defect (ASD) closure and predictors of unremitting NOM. The pathogenic role of migraine biomarkers such as calcitonin gene‐related peptide (CGRP) and neuropeptide Y (NPY) were also assessed.BackgroundNew‐onset migraine has been observed after transcatheter ASD closure. Neuropeptides like CGRP and NPY stored both in the brain and heart are implicated in migraine pathophysiology. The potential role of those migraine biomarkers in NOM, as well as the risk factors and long‐term outcomes of NOM, remain largely unknown.MethodsWe enrolled patients without previous migraine who underwent successful transcatheter ASD closure between 2001 and 2013. The parameters of transthoracic echocardiography, and plasma CGRP and NPY levels measured by enzyme‐linked immunosorbent assay, were collected prospectively before and after ASD closure, and compared between patients with NOM and those without. Predictors of NOM were assessed. Telephone interviews were performed in 2022 to assess migraine status. Clinical and procedural characteristics were compared between patients with unremitting migraine and those with transient migraine that remitted within 1 year.ResultsOf the 212 patients (median age, 21 years; 75.9% female), 43 (20.3%) had NOM. Potential predictors of NOM included a young age (adjusted odds ratio [aOR] 0.98, 95% confidence interval [CI] 0.96–0.99; p = 0.040), large ASD size (aOR 1.07, 95% CI 1.01–1.14; p = 0.022), and transient residual shunting after closure (aOR 2.78, 95% CI 1.05–7.36; p = 0.039). Post‐closure plasma CGRP levels, but not NPY levels, were significantly higher than pre‐closure levels (47.9 vs. 38.0 pg/mL, p = 0.023) among patients with NOM. Of the 27 patients with migraine who reported their migraine status at a median 14‐year follow‐up, 13 (48.1%) had unremitting migraine. Patients with unremitting migraine were more likely to have a smaller device‐to‐ASD size ratio (1.21 vs. 1.33, p = 0.039) and a larger pulmonary flow‐to‐systemic flow ratio (2.9 vs. 2.3, p = 0.012) than those with transient migraine.ConclusionsCalcitonin gene‐related peptide may play a pathogenic role in NOM after transcatheter ASD closure. A young age, large ASD size, and transient residual shunting potentially predict migraine occurrence after ASD closure. NOM not reaching remission for years may result from a significant shunt before closure.