Congenital absence of the portal vein (CAPV) is a rare malformation in which intestinal and splenic venous flow bypasses the liver and drains directly into the systemic circulation via a congenital portosystemic shunt. We describe two cases of CAPV presenting as pulmonary hypertension that were initially suspected as primary pulmonary hypertension. However, subsequent ultrasonography and CT detected the absence of a portal vein and the presence of a portosystemic shunt. Pulmonary hypertension is a recognized complication of liver disease and portal hypertension. However, these two cases illustrate that CAPV may result in pulmonary hypertension without liver disease or portal hypertension.