In patients with one anatomical or functional ventricular chamber, which encompasses a spectrum of rare and complex congenital cardiac malformations, a staged surgical approach in view of an ultimate Fontan operation has become the procedure of choice. Especially in the earlier era, perioperative mortality was the leading cause of death. However, many patients have a long and high-quality life, continuously improved by a better understanding of Fontan hemodynamics and the refinement of the surgical procedures. Nevertheless, the prospect of eventual failure of the Fontan circulation remains a major concern. More specifically, evaluation of the pulmonary circulation becomes particularly important as the failing Fontan circulation has become a common indication for cardiac transplantation. Although essential, especially in the preoperative setting, a comprehensive evaluation of the pulmonary circulation remains difficult in this patient population.