Background The aim of this study was to investigate the outcome after extracardiac conduit (ECC) Fontan operation, and the risk factors of Fontan failure. Methods From 1993 to 2010, 279 patients underwent Fontan operation in Asan Medical Center. Of them, 235 children who underwent ECC Fontan operation, were subjects of this study. Gender distribution (M:F) was 141:94. Median age at operation was 3.49 years (range 1.74~28.58 years). Polytetrafluoroethylene tube graft was used (size 16~22mm) throughout except for one patient. Fenestration was created in 24 patients. Fifty seven children had heterotaxia. The ventricular morphology was single left ventricle in 86, single right ventricle in 92 and two balanced ventricles in 57 patients. Bidirectional cavo-pulmonary shunt was preceded in 211 patients. Median duration of follow up was 5.06 years. Coumadine was used for anticoagulation in 203 patients. Actuarial survival rate, failure free survival rate, and the risk factor of it were analysed. Results Actuarial survival rate was 91.0% at 10 years. There were 6 hospital deaths and 9 late deaths. And in 3 patiens, heart transplantation was required later due to failure of Fontan. Failure free survival rate was 87.0% at 10 years. Univariate analysis showed the morphology of ventricles (P =0.0322), anomalies of pulmonary veins (P = 0.0063), pre-operative regurgitation of atrioventricular valves (P < 0.0001), mean pulmonary artery pressure (P < 0.0001), mean left atrial pressure (P = 0.0003), significant collaterals of artery / vein (P < 0.0001), cardiopulmonary bypass time (P < 0.0001), immediate post-operative central venous pressure (P = 0.0015), and post-operative lasting pleural effusion (P < 0.0001) as significant risk factors for failure of Fontan. Fontan risk score was not related to Fontan failure (P = 0.1684). The other complications were thromboembolism in 11 patients, protein-losing enteropathy in 13 patients, arrhythmia in 28 patients. Two hundred fifteen (97.7%) children of survivors were in NYHA functional class I or II. Conclusion Mid-term survival and functional status of patients after an ECC Fontan operation are satisfactory. And for more adequate selection of candidate patient, Fontan risk score remained to be revised.