Conversion of the atriopulmonary Fontan to a total cavopulmonary extracardiac connection with concomitant arrhythmia surgery and pacemaker placement is a safe and efficacious procedure for this patient population. From 1994 to 2007 a total of 118 patients have undergone this procedure with one (0.8%) early and nine (7.6%) late deaths. During the course of our experience with Fontan conversion our surgical strategy has evolved to include various ablative techniques to treat macro re-entrant atrial tachycardia, focal (automatic) atrial tachycardia, atrioventricular nodal reentry tachycardia, atrial tachycardia due to accessory connections, atrial fibrillation, and ventricular tachycardia. The various mechanisms that we use to treat the underlying atrial arrhythmias are described in this review. We have also encountered patients with variations of the Fontan and other complex anatomic and pathophysiologic aberrations who were not amenable to standard takedown and ablative procedures. We describe those circumstances and the solutions we found to treat those patients.