Patients with primary sclerosing cholangitis (PSC) are at an increased risk for biliary tract carcinoma. The preoperative diagnosis of a biliary tract tumor as a malignancy is difficult, even using new modalities such as multidetector computed tomography (MD-CT), magnetic resonance cholangiopancreatography (MRCP), endoscopic retrograde cholangiography (ERC), and (18)F-fluorodeoxyglucose positron emission tomography (FDG-PET). Surgery is considered to be first line of treatment when these examinations suggest the presence of malignancy in the biliary tract, depending on both the curability of the cancer and the impaired liver function due to PSC. The management of gallbladder masses in patients with PSC remains problematic due to difficulties with the precise diagnosis and adequate surgery. Xanthogranulomatous cholecystitis (XGC) is a type of chronic cholecystitis, and sometimes coexists with gallbladder cancer. It is very difficult to make a preoperative diagnosis differentiating these two diseases. This report presents the case of a patient with XGC, who had been suspected of having gallbladder cancer before surgery, because the tumorous lesion emerged within a year and showed a focally increased uptake by FDG-PET during the follow up for PSC for years. This is the first case of XGC discovered during treatment for PSC.