Congenital heart disease accounts for 40% of pediatric heart transplants and presents unique challenges to the transplant team. Suitability for transplantation is defined in part by degree of sensitization, pulmonary vascular resistance, and hepatic reserves. The incremental transplant risk for patients with congenital heart disease occurs within the first 3 months, after which survival is equivalent to transplantation for cardiomyopathy. Single ventricle with prior palliation, and especially the failing Fontan, carry the highest risk for transplantation and are least amenable to bridging with mechanical circulatory support. More effective bridging to transplant with mechanical circulatory support will require improvements in the adverse event profile of available pumps and the introduction of miniaturized continuous flow technology. The major barriers to routine long-term survival are chronic allograft failure and allograft vasculopathy. Despite these many challenges, continuing improvements in the care of pediatric heart transplant patients have pushed the median posttransplant survival past 15 years for children and to 20 years for infants.