Objectives. This study was undertaken to determine those factors that may influence survival in patients with heterotaxy syndrome undergoing the Fontan procedure.Background. The Fontan procedure remains the preferred palliative procedure for patients with heterotaxy syndrome. Although the mortality rate has improved for patients without this syndrome undergoing the Fontan procedure, it remains high for patients with heterotaxy syndrome.Methods. The medical records of 20 consecutive pediatric patients with asplenia (n = 12) and polysplenia (n = 8) who underwent the Fontan procedure between January 1, 1986 and December 31, 1990 were reviewed. Anatomic and hemodynamic data were collected, as well as data on types of surgical palliative procedures and on outcome of the Fontan procedure.Results. There were two early and two late deaths for a total mortality rate of 20% in the patients with heterotaxy syndrome, as compared with 8.5% for the patients without this syndrome who underwent the Fontan procedure during the same time period. Factors that significantly increased the risk of the Fontan procedure in these patients were 1) preoperative findings of greater than mild atrioventricular valve regurgitation, b) hypoplastic pulmonary arteries, and c) mean pulmonary artery pressure ≥ 15 mm Hg after 6 months of age. Systemic and pulmonary venous anomalies coupled with single-ventricle anatomy were not significant risk factors for determining a poor outcome of the Fontan procedure.Conclusions. This study suggests that the outcome of the Fontan procedure in patients with heterotaxy syndrome may be improved by early protection of the pulmonary vascular bed, despite the existence of other cardiac anomalies.