A retrospective study was undertaken of 157 patients who underwent a Glenn anastomosis between January 1996 and May 2001. Of these, 33 had heterotaxy syndrome: 20 males and 13 females, with a mean age of 1.26 +/- 2.8 years. Twenty-five had right atrial isomerism and 5 had left isomerism. A common atrioventricular valve was found in 24 patients, 18 had bilateral superior venae cavae, and 18 had anomalous pulmonary venous return. Repair was carried out in 8 patients with anomalous pulmonary venous return, and pulmonary artery augmentation was performed in 11. Compared to the 124 patients who had a Glenn operation for single ventricle without heterotaxy, there were significantly longer durations of mechanical ventilation, intensive care unit stay, and inotropic support, as well as higher mortality in the heterotaxy group. Heterotaxy syndrome with single ventricle still has a high rate of morbidity and mortality. Patients with severe atrioventricular valve regurgitation are at risk of early death. Complete Fontan circulation may not be possible in all patients, and Glenn anastomosis may be their final palliation.