A 50-year-old male patient was admitted to the hospital because of fatigue and a palpable abdominal mass. The diagnoses of chronic renal failure and portal vein thrombosis were established by specific investigations. Incidentally, junction of the cystic duct with the left hepatic duct and absence of the common bile duct were found during endoscopic retrograde cholangiopancreatography study. To the authors' knowledge, this is the first reported case of an absence of the common bile duct and junction of the cystic duct with the left hepatic duct in a patient with chronic portal vein thrombosis. Such lesions may cause unexpected complications during biliary surgery.