Ischemic-type biliary lesions (ITBLs) are the most frequent cause of nonanastomotic biliary strictures in liver grafts, affecting about 2-19 % of patients after liver transplantation. ITBL is characterized by bile duct destruction, subsequent stricture formation, and sequestration. We report here the case of a patient affected by extremely severe ITBL, with sequestration and disintegration of the entire bile duct system, in which it was possible to extract the complete biliary tree endoscopically in a single piece. Histological examination revealed that all cells of the bile duct wall had been destroyed within 3 months after liver transplantation and replaced by connective tissue. Subsequently, biliary stricture formation occurred at the hepatic hilum, as well as the adjacent large bile ducts. It may be hypothesized that cellular rejection of small bile ducts leads to the vanishing bile duct syndrome, whereas cellular rejection of large bile ducts results in ITBL. The strictures were repeatedly dilated by endoscopic means, allowing successful control of stricture formation, as well as maintenance of liver function. At the time of writing, the grafted organ and the patient had survived for more than 3 years in good health. This is the first detailed report on a sequestration of the entire bile duct system caused by ITBL, successfully treated for several years by endoscopic means.