Background Patients with atriopulmonary Fontan tend to undergo conversion to total cavopulmonary connections secondary to arrhythmias or poor flow dynamics. However, the ideal candidate is unknown. Methods Between December 1994 and May 2011, 70 patients (40 males [57%]) underwent Fontan conversion. Median age was 23 years (range, 4 to 46 years). Excluded were 1.5 ventricle conversions. The most common diagnoses included tricuspid atresia in 34patients (49%) and double-inlet left ventricle in 16 (23%). Atrial tachyarrhythmia was present in 62 patients (89%), 41 (59%) had atrioventricular valve (AVV) regurgitation, and 32 (46%) were in New York Heart Association class III or IV. Atriopulmonary Fontan was the original connection in 58 patients (83%), whereas the Björk modification was performed in 8 (11%). Results Fontan was performed with an intraatrial conduit in 41 patients, an extracardiac conduit in 18, and a lateral tunnel in 11. Forty-nine patients (70%) underwent concomitant arrhythmia operations. Early death occurred in 10 patients (14%). Multivariate analysis revealed age older than 27 years (p = 0.009), AVV regurgitation (p = 0.016), lack of arrhythmia operation (p = 0.04), and male sex (p = 0.02) were predictors of perioperative death. Mean follow-up was 5 years (maximum, 17 years). Overall survival at 1, 5, and 10 years was 81%, 70%, and 67%, respectively, and 84% of patients were in New York Heart Association class I or II. Conclusions Proper selection of Fontan conversion candidates is critical. Concomitant arrhythmia operations may be associated with improved survival. Older age and AVV regurgitation increase the risk of poor outcome, and cardiac transplantation may be a better option.