Background: Historically the Fontan operation in patients with single ventricle and heterotaxy syndrome has been associated with high mortality because of systemic or pulmonary anomalous venous drainage, incompetent common atrioventricular valve, right ventricle type univentricular heart, and arrhythmia. Material and Method: A retrospective review of 62 patients $(age:;54.79pm33.97;months)$ with heterotaxy syndrome who underwent a extracadiac Fontan operation between 1996 and 2005 was performed. Twenty one patients had left atrial isomerism, and 41 had right isomerism. The Fontan procedure was staged in all but 2 patients, and a fenestration was less placed in left isomerism. Result: Left isomerism was associated more with interrupted inferior vena cava and pulmonary arteriovenous fistula, and right isomerism was associated more with anomalous pulmonary venous drainage, common atrioventricular valve and morphologic right ventricle. There were 3 hospital deaths$(4.8\%)$ and 3 late deaths $(5.2\%)$ with a follow-up duration of $48.8pm31.0$ months. Eight-year survivals were $90.5pm6.4\%$ in left isomerism and $88.6pm5.4\%$ in right isomerism (p=0.94). At 8 years, freedom from reoperation was $73.9pm11.3\%$ in left isomerism, and $82.3pm6.7\%$ in right isomerism (p=0.87). Atrioventricular valve regurgitation progressed after Fontan operation in heterotaxy syndrome, and reoperation for pulmonary arteriovenous fistula and permanent pacemaker implantation for sinus node dysfunction were required more in left isomerism. Conclusion: The extracardiac Fontan operation can now be performed in patients with heterotaxy syndrome with excellent survival. However, morbidity in terms of postoperative atrioventricular valve regurgitation, arrhythmia, and pulmonary arteriovenous fistula remains significant.