The purpose of this study was to compare the outcomes of lateral tunnel (LT) and extracardiac conduit (ECC) Fontan procedures at a single institution. From April 1995 to December 2006, 165 Fontan procedures were performed (67 LT, 98 ECC). Pre-, intra- and postoperative variable values were compared between two different techniques. Operative mortality was 5 (3 LT, 2 ECC). Immediate postoperative transpulmonary gradient (LT 8.5+/-ECC 2.5 vs. 6.6+/-2.4 mmHg) and central venous pressure (LT 18.3+/-3.8 vs. ECC 15.6+/-2.4 mmHg) showed significant difference (P<0.001). The LT patients had a higher incidence of sinus node dysfunction in the postoperative period (22.4% vs. ECC 11.2%; P=0.05). Mean follow-up was 74.1+/-31.5 months in LT, and 31.7+/-28.1 months in ECC patients. There was one late death. Actuarial survival at 10 years is 92% for LT, and 89% for ECC patients (P=0.796). The LT and ECC, both, showed comparable early and mid-term outcomes in operative morbidity and mortality, postoperative hemodynamics, survival. Use of ECC for modified Fontan operation reduces the risk of sinus node dysfunction and shows better outcome of immediate postoperative hemodynamics.