A 56-year-old man was admitted to our hospital with a diagnosis of hilar bile duct cancer. Abdominal ultrasonography, computed tomography and endoscopic retrograde cholangiopancreatography showed no other concomitant disease. Biochemical data showed 0.6 mg/dL of total bilirubin, 104 IU/L of alanine aminotransferase and 469 mg/dL of alkaline phosphatase. Carbohydrate antigen 19-9 was elevated as 112.1 U/mL. Operative findings included a resectable left hilar bile duct cancer and grayish-white nodules 0.3-0.5cm in diameter on the surface of segments 6 and 4 of the liver. Although intrahepatic metastasis of the bile duct cancer was highly suspected under intraoperative US, frozen section was reported to show the small nodules containing multiple biliary hamartomas, so-called von Meyenburg complex. Therefore, a left hepatic lobectomy together with resection of the extrahepatic bile duct followed by a Roux-en-Y hepaticojejunostomy was the procedure of choice. His postoperative course was uneventful. The intraoperative findings could have been misdiagnosed due to their similarity to intrahepatic metastasis and intraoperative histology is indispensable to differentiate von Meyenburg complex in this case. The possibility of a preoperative imaging diagnosis for von Meyenburg complex seems to depend on the size of the bile duct structure in each hamartoma. To the best of our knowledge, this is the fourteenth case of bile duct cancer associated with von Meyenburg complex reported in the literature. The following case is being reported because of the rarity of the disease and to stress the importance of intraoperative histology to avoid misdiagnosis as the disseminated disease, particularly when malignant neoplasia is surgically treated.