The Fontan procedure has been a significant contribution to the therapeutic armamentarium of congenital heart surgeons for the treatment of single ventricle anomalies. However, it has its limitations. Patients may have failure of the Fontan circulation acutely postoperatively or late during the long-term follow-up. Early failure is often related to an intraoperative myocardial injury or unsuspected elevated pulmonary vascular resistance; this has a very high mortality. Late failure of the Fontan procedure may present with symptoms typical for heart failure. However, protein-losing enteropathy is another condition related to late failure of the Fontan operation. Late failure may be related to a number of different factors, many of which are amenable to reoperation. Every effort should be made to identify which hemodynamic factors are responsible for late failures. However, cardiac transplantation will likely be necessary for the majority of patients.