While the Fontan operation has facilitated the survival of a generation of children born with congenital heart disease resulting in a functional single ventricle, it does not recreate a normal circulation. Over time, survivors of the Fontan operation are at risk for ventricular dysfunction, plastic bronchitis, protein-losing enteropathy and chronic Fontan failure. New techniques and therapies are emerging to address the long-term risks associated with Fontan physiology, but as the number of survivors continues to grow, the recognition of the limitations of this circulation is increasing. Novel investigations of possible mechanical devices designed to function as a subpulmonary ventricle are underway, but are still many years away from clinical use. In the meantime, continued development of medical therapeutics targeted at the specific problems of the Fontan circulation will be beneficial and might reduce the need for cardiac transplantation.