A 65-year-old female presenting with hepatobiliary cystadenoma (HC) comprised of multiple cysts in the liver and a non-specific epigastric pain is reported herein. Ultrasound study demonstrated dilated common bile duct (CBD) and intrahepatic bile ducts, plus two spherical stone-like bodies filling defects in the proximal CBD. Sphincterotomy and basket performed for the patient were not successful. Upon surgery, two cystic masses were found in CBD and were resected. Histopathological examinations showed hepatobiliary cystadenoma with mesenchymal stroma.