The Fontan circulation, accomplished by direct surgical connection of the vena cavae to the pulmonary arteries, can be an effective palliation for patients with a single ventricle. However, failure of the Fontan circulation can result from mechanical obstruction, cardiac arrhythmias, increasing pulmonary vascular resistance, or deteriorating ventricular performance. Although systolic ventricular failure can usually be identified by a combination of clinical signs, symptoms, and imaging findings, diastolic ventricular dysfunction is likely an underrecognized cause of Fontan failure. Methods for detection of impaired diastolic function in a single ventricle are evolving, and established techniques appropriate in the biventricular heart lack validation in single ventricle. Association of biomarkers, cardiac magnetic resonance, and echocardiographic findings with invasively acquired pressure-volume loop data in humans may offer a way forward to accurate, noninvasive diagnosis. Today, therapy for severe diastolic ventricular dysfunction in the Fontan circulation is often disappointing and may require consideration of a ventricular assist device or even cardiac transplant. Progress toward improved outcomes of the Fontan palliation likely depends on successful innovation in primary prevention strategies and the development of more effective pharmacotherapy.