OBJECTIVE The extracardiac conduit procedure is widely used for patients with heterotaxy syndrome with complex systemic and pulmonary venous anomalies; however, it lacks conduit-growth potential and requires long-term anticoagulation. We present the intracardiac Fontan procedure, which eliminates the above-mentioned disadvantages. METHODS Twenty-four patients (mean age, 4.1 years; weight, 13.0 kg) with heterotaxy syndrome underwent intracardiac Fontan operations between March 1995 and March 2008. In each patient, the anomalous systemic venous return with the isolated hepatic vein was redirected to the pulmonary artery using an intra-atrial baffle without obstructing the pulmonary venous pathway; this was accomplished by anterior (n=5), lateral (n=15) or posterior tunnel methods (n=4), depending on the anatomical relationship of the systemic and pulmonary venous pathways. RESULTS There was one (4%) in-hospital and two (8%) late deaths in total. Five (21%) patients underwent re-operation for either pulmonary venous obstruction or supraventricular tachycardia. The actuarial 12-year survival was 86% (the Kaplan-Meier survival plot). The freedom from re-operation at 10 years was 77%. Anticoagulation was not required except for two patients (8%) who had prosthetic valves and coagulation disorder. Obstruction of the systemic venous pathway was not observed in any patient; however, five (20%) patients had clinically significant postoperative arrhythmias. At the final follow-up, all survivors were categorised as the New York Heart Association class I. CONCLUSIONS Aided by detailed preoperative anatomical and physiological diagnoses, intracardiac Fontan procedures were technically feasible in patients with complex systemic and pulmonary venous anomalies. The specific cardiac anatomy in these patients warranted this procedure; however, taking into consideration the improved outcomes of the modified Fontan procedure, this method should be performed with deliberation.