With longer duration of follow-up, as many as 50% of Fontan patients will develop atrial tachycardia, usually in association with significant hemodynamic abnormalities. Arrhythmia management in the Fontan patient is reviewed. The incidence and type of arrhythmia occurrence are examined, including macro-reentrant rhythm which involves the right atrium, reentrant rhythm localized to the pulmonary venous atrium (seen in patients with lateral tunnel procedures), and atrial fibrillation. Risk factors for development of these arrhythmias are considered, and short- and long-term therapeutic options for medical and surgical treatment are discussed. Surgical results are presented for 117 patients undergoing Fontan conversion and arrhythmia surgery (isthmus ablation (9), modified right atrial maze (38) or Cox-maze III (70)). Operative mortality is low (1/117, 0.8%). Seven late deaths occurred, and include two patients who died shortly following cardiac transplantation (2/6, 33%) after Fontan conversion and arrhythmia surgery. Overall arrhythmia recurrence is 12.8% during a mean follow-up of 56 months. Fontan conversion with arrhythmia surgery can be performed with low operative mortality, low risk of recurrent tachycardia, and marked improvement in functional status in most patients. Because the development of tachycardia is usually an electromechanical problem, attention to only the arrhythmia with medications or ablation may allow progression of hemodynamic abnormalities to either a life-threatening outcome or a point at which transplantation is the only potential option. Because cardiac transplantation in Fontan patients is associated with high early mortality, earlier consideration for surgical intervention is warranted.