Intrahepatic stone disease poses a difficult postoperative management problem due to frequent stone recurrence. Most of the methods proposed for long-term access to the intrahepatic biliary tree require multiple sessions of additional, usually invasive, procedures. An alternative method for endoscopic long-term access to the intrahepatic ducts, represented by a side-to-side anastomosis between the isolated Roux-en-Y jejunal limb of the bilioenteric bypass and the duodenum (duodenojejunostomy), was used in eight patients with retained and/or recurrent stones after surgical treatment of intrahepatic stone disease. There were no short- or long-term complications or mortality associated with the duodenojejunostomy. Postoperative endoscopic access to the intrahepatic ducts was successfully achieved in five of six patients: one with stone recurrence, one with a left hepatic duct stricture and stone recurrence and one with known retained postoperative stones. In two patients, no stones were found at endoscopy. Side-to-side duodenojejunostomy may be useful in the long-term endoscopic management of recurrent intrahepatic biliary stone disease and should be indicated whenever a bilioenteric anastomosis is performed for the treatment of bilateral intrahepatic stone disease.