Polysplenia syndrome is a rare congenital disease with multiple spleens and complex anomalies of internal organs and vessels. Multiple intrahepatic gallstones occurred in an adult patient. Imaging studies revealed polysplenia, a shortened pancreas, and absence of a segment of the superior vena cava. Extensive gallstones in the liver and bile duct abnormalities were confirmed intraoperatively. Surgical treatment included partial hepatectomy, bile duct exploration, and insertion of a drainage T-tube. Postoperatively, the patient developed bacteremia, which resolved after targeted antibiotic therapy. The case shows the association of polysplenia syndrome with disorders of the liver and biliary tract. It emphasizes the need for a thorough anatomical examination, early detection of biliary complications and regular follow-up of patients.