Protein-losing enteropathy (PLE) is a poorly understood and enigmatic disease process affecting patients with single ventricle after Fontan operation. In those afflicted, PLE after Fontan operation results in significant morbidity and mortality. The pathophysiology of the disease is unknown; however, a proposed mechanism incorporates a combination of phenomena including: (1) altered hemodynamics, specifically low cardiac output; (2) increased mesenteric vascular resistance; (3) systemic inflammation; and (4) altered enterocyte basal membrane glycosaminoglycan make-up. A paradigm for the clinical management of PLE after Fontan operation is proposed.