To study the incidence of late postoperative arrhythmias and to assess the possible risk factors related to such arrhythmias after the Fontan operation, we retrospectively reviewed standard 12-lead electrocardiogram (ECG) and Holter monitoring (Holter) of 21 patients who survived the Fontan operation between September 1982 and December 1992. Late postoperative supraventricular arrhythmias were detected in 7 of 21 patients by ECG, and in 10 of 17 patients by Holter. Older patients undergoing the Fontan operation had greater incidence of late postoperative supraventricular arrhythmias than younger patients. Patients undergoing superior vena cava-pulmonary artery anastomosis to prevent the right atrial distension had less incidence of late supraventricular arrhythmias detected by Holter. Thus, supraventricular arrhythmias are common in patients after the Fontan operation and may cause morbidity and mortality. Therefore, it is important to prevent the development of late arrhythmias by procedures designed to reduce atrial pressure at younger age.