A 64-year-old woman who had undergone surgery for gallstones twice was admitted with epigastric pain and fever. Ultrasonography revealed gallstones in the dilated left lateral intrahepatic bile ducts. Abdominal computed tomography disclosed atrophy of the left lateral segment and the right lobe of the liver, and hypertrophy of the left medial segment and the caudate lobe. Percutaneous transhepatic cholangiography demonstrated that the stones were localized in the left lateral intrahepatic bile ducts, and that the choledochoduodenostomy previously established was patent. Percutaneous transhepatic portography revealed that the left portal vein was absent and the left medial segment was supplied by the right portal vein. Left lateral hepatic segmentectomy and release of the choledochoduodenostomy were performed. Postoperative recovery was good, and the patient is now well without any complaint. This report discusses the surgical treatment for intrahepatic stones under very complicated conditions and the relationship between intrahepatic stones and anomalous portal venous system.