We experienced a girl with congenital absence of the portal vein. She was examined by computed tomography (CT), three-dimensional computed tomographic angiography (3DCTA), digital subtraction angiography and liver biopsy. Nodular regenerative hyperplasia of the liver was detected, presumably due to an abnormal hepatocellular response to absent portal flow. 3DCTA showed that the splenic vein and superior mesenteric vein joined to form a common trunk, which directly entered the right atrium. 3DCTA may be a valuable noninvasive tool for identifying portal malformations.