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Abstract Background The term hepatopulmonary syndrome typically applies to cyanosis that results from “intrapulmonary vascular dilatation” due to advanced liver disease. Similar findings may result from a congenital portosystemic shunt without liver disease. An adverse consequence of such shunts is intrapulmonary vascular dilatation, which affects the microvascular gas exchange units for oxygen. Case presentation Here, we describe a toddler with chronic cyanosis, exercise intolerance, and finger clubbing due to a malformation shunt between the portal vein and the inferior vena cava. A transcatheter embolization of the shunt resulted in resolution of his findings. Conclusions Congenital portosystemic shunts need to be considered in the differential diagnosis of cyanosis.