Thirteen patients (ages 4 to 16 years) with univentricular heart of right ventricular type, nine with double-inlet right ventricle (DIRV), and four with mitral atresia who underwent a modified Fontan operation were reviewed. Among those with DIRV, right isomerism with a common atrioventricular (AV) valve was found in eight and situs inversus in one; among those with mitral atresia, AV discordance was found in two and concordance in two. Intra-atrial routing using a baffle with atriopulmonary anastomosis was the main procedure (11 patients). There were two operative deaths (one DIRV, one mitral atresia) and three hospital deaths, with an early mortality of 38.5% overall (DIRV 44%, mitral atresia 25%). Low cardiac output was the main cause of death, with relatively high right atrial pressure and with tachyarrhythmias in most of the patients. Mortality was 75% for patients with DIRV who had total anomalous pulmonary venous drainage (n = 4) and 20% for those without (n = 5). Preoperative ventricular volume and ejection fraction were not different between those with severely low cardiac output (n = 4, three deaths) and the others, whereas ventricular mass/volume ratio was significantly lower in the former group. Two late deaths (one DIRV, one mitral atresia) related to the AV valve regurgitation. These results may indicate a relatively poor outcome after the modified Fontan operation for patients with univentricular heart of right ventricular type as a result of basic anatomic and hemodynamic problems.