Protein-losing enteropathy is a relatively uncommon complication of Fontan procedures for palliation of complex congenital cardiac disease. However, the relative infrequency of protein-losing enteropathy belies the tremendous medical, psychosocial and financial burdens it places upon afflicted patients, their families and the healthcare system that supports them. Unfortunately, because of the complexity and rarity of this disease process, the pathogenesis and pathophysiology of protein-losing enteropathy remain poorly understood, and attempts at treatment seldom yield long-term success. The most comprehensive analyses of protein-losing enteropathy in this patient population are now over a decade old, and re-evaluation of the prevalence and progress in treatment of this disease is needed. This report describes a single institution experience with the evaluation, management, and treatment of protein-losing enteropathy in patients with congenital cardiac disease in the current era, follows with a comprehensive review of protein-losing enteropathy, focused upon what is known and not known about the pathophysiology of protein-losing enteropathy in this patient population, and concludes with suggestions for prevention and treatment.