The authors report 7 cases of late arrhythmias after atriopulmonary (5 cases) or total cavopulmonary (2 cases) bypass procedures. There were 6 cases of atrial flutter and one case of atrial tachycardia. The condition presented with cardiac failure in 5 cases. In 2 patients, atrial flutter caused syncope or dizziness. The arrhythmia was reduced by atrial stimulation (3 cases) or by cardioversion (1 case). Prevention of recurrence with oral amiodarone was effective in all cases but was responsible for secondary effects in 4 cases. In one patient, recurrence of atrial flutter was complicated by right atrial thrombosis with cerebral embolism. Five patients were reoperated after cardiac catheterisation and angiography. Surgery consisted of resection of a stenosis of the anastomosis in one case, and the transformation of atriopulmonary anastomosis into a total cavopulmonary bypass because of a very dilated right atrium without stenosis in 4 patients. The immediate postoperative period was complicated by a recurrence of the arrhythmia in 3 children not treated by antiarrhythmic therapy. At long-term, one patient died 6 months after withdrawal of amiodarone therapy of recurrence of atrial flutter. Five of the 6 survivors are treated with amiodarone or a betablocker; 3 have had pacemaker implantation for severe bradycardia. Late atrial arrhythmias complicating atrio- and cavopulmonary bypass procedures carry a risk of cardiac failure and sudden death. When diagnosed, the patient should be investigated for stenosis of the anastomosis but severe dilatation of the right atrium is often the only finding. After restoration of sinus rhythm, maintenance antiarrhythmic therapy should be continued indefinitely.