Transcatheter closure of secundum atrial septal defect (ASD) and patent foramen ovale (PFO) has become a routine procedure. Little is known about the effect of atrial septal device implantation on the occurrence of atrial fibrillation (AF). We evaluated the frequency of AF occurring after transcatheter PFO and ASD closure in a large population. From 1994 until 2007 a total of 1,062 patients underwent transcatheter closure of an interatrial communication. New-onset AF was defined by 12-lead electrocardiogram or Holter monitoring in patients without a history of AF at baseline. Of the 1,062 patients, 822 had a PFO and 240 had an ASD. During a median follow up of 20 months, new-onset AF was documented in 8% of patients. New-onset AF occurred in 7% of patients after PFO closure and in 12% of patients with underlying ASD. The annual incidence of new-onset AF was 2.5% and 4.1% in patients with PFO and ASD, respectively. Generally, patients with new-onset AF were older than those without AF. Device type or size did not influence the occurrence of AF. In the group of patients with PFO, residual shunt was more common in patients with AF compared with the non-AF group. In conclusion, AF is more common after PFO and ASD closure compared with the general population; although device type or size did not impact the occurrence of AF, residual shunt may influence the occurrence of AF after intervention in patients with underlying PFO.