The heterotaxy syndromes are characterized by a high incidence of cardiac anomalies of extreme heterogeneity. Due to this, the surgical management is varied and challenging. Although a minority of patients can undergo biventricular repair, the complexity of the cardiac defects, and the high incidence of ventricular hypoplasia, mandate a surgical approach in the majority of patients depending on the creation of a functionally univentricular heart. Traditionally, the functionally univentricular approach was associated with a high mortality. More recently, the results have been improving as a result of better understanding of these malformations, and logical improvements in surgical technique. In this review, we will make brief comments on the nomenclature and classification of the heterotaxy syndromes, and the range of cardiac anomalies, before concentrating on the surgical treatment for those patients having functionally univentricular hearts in the setting of heterotaxy. More specifically, we will review initial palliation in early life, creation of the cavopulmonary anastomoses, including the Kawashima procedure and the Fontan circulation, and the role of transplantation.