The Fontan operation allows for longer survival of those born with functionally single ventricle physiology. Although it effectively eliminates cyanosis, increased systemic venous pressure is an unavoidable consequence and low cardiac output is frequent. The abdomen is particularly vulnerable to these alterations in hemodynamics because the hepatic blood flow consists predominantly of portal venous flow, which relies on a low pressure gradient between the portal and hepatic veins. Therefore, any subtle increase in systemic venous pressure will adversely affect the hemodynamic balance of the liver as well as the intestine. As the clinical manifestations and routine laboratory findings of abdominal complications can lag behind the hemodynamic and pathologic changes in the abdominal organs, regular imaging surveillance is critical. Magnetic resonance (MR) provides excellent visualization of both cardiovascular and abdominal systems. It provides robust anatomic and hemodynamic data which can be used for timely implementation of treatment options. In this review paper, we discuss the pathogenesis and MR findings of abdominal complications following the Fontan operation. Specifically we explore the utility of phase-contrast MR for assessment of the abdominal circulation in children following the Fontan palliation.