This study was designed to compare reduced heart rate variability (HRV) in children with atrial septal defect (ASD) after surgical ASD closure with interventional (Amplatzer device) closure. Reduced HRV was observed in all children with ASD before treatment. HRV was further impaired 1 month after surgical ASD closure but not after catheter device closure. Three months after treatment, HRV indexes tended to normalize in both groups.