Aims Persistent iatrogenic atrial septal defect (iASD) after transseptal puncture for pulmonary vein isolation (PVI) has been described recently as a complication of PVI. No data exists evaluating systematically the incidence and clinical implications of iASDs after PVI using a remote robotic navigation system (RNS) with sheaths with a distinct larger outer diameter. Methods and results In this prospective study, 40 patients with either paroxysmal (n = 22, 55%) or persistent symptomatic atrial fibrillation were treated with circumferential PVI using an RNS. In all patients, a single-puncture, double-transseptal approach was used to access the left atrium. Transoesophageal echocardiography was performed before and the day after PVI as well as after a 3 and 6 months follow-up (FU). The day after ablation an iASD was detected in 38 of 40 (95%) patients with a mean diameter of 3.45 ± 1.5 mm. At 6-month FU, the iASDs were closed in 30 of 39 (78.9%) patients. During the 6-month FU period, no patient died or suffered from cerebral or cardiac embolism. Conclusion After a single-puncture, double-transseptal approach for PVI using the RNS, iASDs show a high spontaneous closure rate of 78.9% after a 6-month FU period. Persistent iASDs following PVI with the RNS are not associated with an increased rate of paradoxical embolism or with relevant shunting.