The Fontan procedure has undergone many modifications since first being performed on a patient with tricuspid valve atresia in 1968. It is now the procedure of choice for individuals born with single-ventricle physiology or for those in whom a biventricular repair is not feasible. Forty years of experience with the Fontan procedure have gradually revealed the shortfalls of such a circulatory arrangement. Sequelae related to the underlying congenital anomaly or to the altered physiology of passive, nonpulsatile flow through the pulmonary arterial bed can result in failure of the Fontan circulation over time. Liver abnormalities including abnormalities in the clotting cascade have been well documented in Fontan patients. The clinical significance of these findings, however, has remained poorly understood. As Fontan survivors have increased in age and number, we have begun to better recognize subclinical hepatic dysfunction and the contribution of liver disease to adverse outcomes in this population. The purpose of this review is to summarize the existing data pertaining to liver disease in the Fontan population and to identify some questions that have yet to be answered.