The Fontan procedure provides a means of separating the systemic and pulmonary circulations in patients with congenital heart defects characterized by a functionally single ventricle. The procedure has undergone numerous changes since its introduction 25 years ago. Technical modifications have now increased its applicability to virtually all forms of univentricular atrioventricular connection, as well as many hearts with biventricular connections. More recently, philosophical changes have been introduced to address increased rates of morbidity and mortality observed in certain subsets of patients. These changes appear to have improved short- and midterm results. The purpose of this review is to offer our strategy for management of such patients. We will discuss the interrelationship between the bidirectional Glenn and Fontan procedures. We will also focus on a number of observations concerning the possible role of accessory pulmonary blood flow, aortopulmonary collateral arteries, and endocrinologic changes.