Background: Therapy of Caroli's syndrome usually consists of endoscopic stone removal in order to achieve adequate bile flow and to avoid secondary complications such as cholangitis or deterioration of liver function. If primary endoscopic treatment is not sufficient, liver resection or transplantation could become necessary to achieve a stone-free situation. Case Report: We herein describe a case of bilobular Caroli's syndrome which was primarily endoscopically treated. Due to a common bile duct stricture after cholecystectomy and choledochotomy 10 years before, endoscopic stone removal was impossible. Instead of liver resection or transplantation, we performed a wide side-to-side choledochoduodenostomy which allowed subsequent endoscopic treatment with successful removal of all bile duct stones during repeated sessions. Six years after surgery, no further episodes of cholangitis have occurred, and the patient has fully recovered with normal liver function. Conclusion: Even bilobular Caroli's syndrome refractory to primary endoscopic treatment might be removed using an interdisciplinary approach thereby successfully avoiding liver resection or transplantation.