ObjectiveTo summarize the cardiac-vascular abnormalities and clinical results in patients with Fontan operation for heterotaxy syndrome. MethodWe retrospectively analyzed the medical records of 81 patients who underwent the Fontan operation with heterotaxy syndrome between September 2008 and September 2013. There were 49 male and 32 female patients at age of 3.79 (range 2.07-13.02) years with preoperative room air saturation of 81% (range 63%-97%) and weight of 14.8 (10.0-36.0) kg. ResultsThere were 70 patients in the right atrial isomerism group and left in 11 patients. Dextrocardia was seen in 16 patients, and single atrium in 50 patients. Single ventricle was found in 44 patients, conotruncal defects in 40 patients, pulmonary stenosis in 72 patients, pulmonray atresia in 8 patients, common atrioventricular valve in 61 patients, and bilateral superior vena cava in 54 patients. The staged Fontan procedure was applied in 57 patients and one stage in 24 patients. Operation strategies were included intra/extracardiac conduit (n=17), extracardiac conduit (n=48), lateral tunnel (n=14) and direct cavopulmonray connection (n=2).There were 15 early deaths. Postoperative complications included low cardiac output in 15 patients, hepatic insufficiency in 35 patients, renal insufficiency in 55 patients required peritoneal dialysis and arrhythmia in 28 patients. The room air saturation was 89% (range 78%-98%) before discharge and time of follow-up was from 2 months to 6 years in 64 patients. Thromboembolic events were found in 2 patients who had accomplished conduit replacement operation. ConclusionCompared with reported literatures in western countries, heteraotaxia patients are mostly with right atrial isomerism. Fontan palliation is still the main treatment option and strict indication was needed for satisfactory clinical results.