The Fontan operation for single ventricle palliation consists of the creation of a complete cavopulmonary connection, usually by incorporating inferior vena caval flow into a pulmonary arterial circulation already receiving flow from the superior vena cava. In single ventricle palliated in this way, the anatomy is complex, and the pathophysiological complications are frequent; so, cardiac imaging is a key aspect of clinical surveillance. Common problems that echocardiography and MRI may disclose and characterise in the Fontan palliation of single ventricle include obstruction of systemic venous and pulmonary arterial flow, atrioventricular and semilunar valve dysfunction, unintended collateral flow patterns, ventricular dysfunction, aortic arch obstruction, interatrial obstruction, fenestration flow and patch leaks. Despite the broad scope of these modalities for detection of such problems, often no single imaging method is comprehensive in any given patient. Therefore, physicians must recognise the limitations of each modality, and circumvent these by application of suitable alternatives. New imaging tools are becoming available, which may ultimately prove to be of value in the Fontan circulation. Proper application of diverse new technologies such as four dimensional flow, computational fluid dynamics and three-dimensional printing will require critical evaluation in the single ventricle population.