OBJECTIVE To determine the clinical features in patients with double inlet right ventricle (DIRV) and separate atrioventricular (AV) valves in terms of the Fontan procedure. METHODS Surgical procedures were carried out in 31 patients with this rare malformation. Their clinical characteristics were compared with similar features in 45 patients with double inlet left ventricle (DILV), 93 with common inlet right ventricle (CIRV), and 20 with common inlet left ventricle (CILV). RESULTS Pulmonary atresia with the right and the left pulmonary arteries being confluent was seen in 58% of patients with DIRV, and pulmonary atresia with non-confluent pulmonary arteries in 15% (P=0.0001). The incidence of these findings was significantly higher when compared with DILV (P=0.0001). Reflecting these morphologic features, constructions of systemic-to-pulmonary shunts and extensive plasty to the pulmonary arteries were more frequently needed in patients with DIRV than in the others (P=0.04, 0.0001). The AV valves have become moderately or severely regurgitant in three with DIRV (10%). The Fontan procedure has thus been employed in 21 with DIRV (64%), this incidence being significantly higher than that seen in the CIRV (37%) group (P=0.01). Survival rate of 95% at 10 years in this group was as excellent as that in the DILV group, and obviously better than that in either CIRV or CILV (P=0.002). CONCLUSIONS Although multiple palliative procedures might be frequently needed to maintain pulmonary perfusion, the Fontan circulation can be justifiably established in patients with DIRV, and regurgitation across the AV valves was not very common.