BACKGROUND: Atrial arrhythmias and progressive circulatory failure frequently develop in patients with a Fontan circulation. Improvement of flow dynamics and revision of the arrhythmia substrate may improve outcomes in selected patients. We sought to determine intermediate-term outcomes after Fontan conversion with arrhythmia operations and identify characteristics associated with decreased transplant-free survival. METHODS: The first 140 Fontan conversions with arrhythmia operations at a single institution were analyzed for predictors of cardiac death or transplant and incidence of arrhythmia recurrence. RESULTS: The median age at the Fontan conversion operation was 23.2 years (range, 2.6 to 47.3 years). Preoperative arrhythmias were present in 136 patients: right atrial tachycardia in 48 patients, left atrial tachycardia in 21, and atrial fibrillation in 67. Freedom from cardiac death or transplant was 90% at 5 years, 84% at 10 years, and 66% at 15 years. The median age at the last follow-up among survivors was 32 years (range, 15 to 61 years). By multivariable analysis, risk factors for cardiac death or heart transplantation were a right or indeterminate ventricular morphology, cardiopulmonary bypass time exceeding 240 minutes, ascites, protein-losing enteropathy, or a biatrial arrhythmia operation at the time of conversion. Freedom from recurrence of atrial tachycardia was 77% at 10 years. Among 67 patients with atrial fibrillation undergoing biatrial arrhythmia operations, none had recurrent atrial fibrillation. CONCLUSIONS: Freedom from cardiac death or transplant for patients undergoing Fontan conversion with an arrhythmia operation is 84% at 10 years. The effects of atrial arrhythmia operations are durable in most patients. These outcomes may serve as useful benchmarks for alternative management strategies.