The principles of Fontan conversion with arrhythmia surgery are to restore the cardiac anatomy by converting the original atriopulmonary connection to a total cavopulmonary artery extracardiac connection and treat the underlying atrial arrhythmias. Successful outcomes of this procedure are dependent on a thorough understanding of several factors: the patient's fundamental diagnosis of single-ventricle anatomy, the resultant cardiac configuration from the original atriopulmonary Fontan connection, right atrial dilatation that leads to atrial flutter or fibrillation, and associated congenital cardiac anomalies. The purpose of this article is to present some of the more challenging anatomic and electrophysiologic problems we have encountered with Fontan conversion and arrhythmia surgery and the innovative solutions we have used to treat them. The cases reviewed herein include: takedown of a Bjork-Fontan modification, right ventricular hypertension and tricuspid regurgitation after atriopulmonary Fontan for pulmonary atresia and intact ventricular septum, takedown of atrioventricular valve isolation patch for right-sided maze procedure, resultant hemodynamic considerations leading to intraoperative pulmonary vein stenosis after Fontan conversion, unwanted inferior vena cava retraction during the extracardiac connection, right atrial cannulation in the presence of a right atrial clot, distended left superior vena cava causing left pulmonary vein stenosis, dropped atrial septum, and the modified right-sided maze procedure for various single-ventricle pathology. Since 1994 we have performed Fontan conversion with arrhythmia surgery on 109 patients with a 0.9% mortality rate. We attribute our program's success in no small measure to the strong collaborative efforts of the cardiothoracic surgery and cardiology teams.