Background: Refractory atrial arrhythmias in patients late after the Fontan operation result in significant morbidity and mortality. We reviewed our experience with arrhythmia surgery in patients who had Fontan operation. Material and Method: Between July 1986 and December 2003, 275 early survivors after Fontan operation were reviewed. Fourteen patients underwent. arrhythmia surgery at reoperation after Fontan operation, and mean age at reoperation was 16.8$pm$7.1 (range: 4.5 ∼ 30.6) years. Mechanisms of arrhythmia included atrial flutter in 8 patients, and atrial fibrillation in 2. Arrhythmia surgery has evolved from isthmus cryoablation in 12 patients to right-sided maze in 2 patients. Thirty-two patients. underwent prophylactic isthmus cryoablation concomitantly at initial Fontan operation. Result: Postoperative arrhythmias occurred in 68 patients (24.7%) among 275. There was no early and late mortality after the arrhythmia surgery. After redo Fontan operation, all patients maintained normal sinus rhythm. Atrial flutter recurred in 3 patients who had sinus conversion with medication and 7 required permanent pacemakers with a mean follow-up of 26.5$pm$29.1 (range: 2 ∼ 73) months. All patients have improved to NYHA class I or II. After prophylactic cryoablation at initial Fontan operation, 29 patients (90.6%) had sinus rhythm, 1 patient had junctional tachycardia, 1 patient had sinus nodal dysfunction, and 1 patient had AV block with a mean follow-up of 51.3$pm$19.8 (range: 4∼80) months. Conclusion: Redo Fontan operation, and concomitant arrhythmia surgery reduced atrial arrhythmias and improved NYHA functional classification.