In the era of laparoscopic cholecystectomy and advanced non-invasive imaging studies, pre-operative endoscopic retrograde cholangiopancreatography (ERCP) for bile duct stones should be reserved for selected patients. ERCP remains the therapy of choice for removal of bile duct stones in the post-cholecystectomy patient and in patients with intact gallbladders. Bile duct stones can be cleared in nearly all patients using endoscopic techniques of sphincterotomy and mechanical lithotripsy. Difficult or complex bile duct stones can be endoscopically removed in the majority of patients with additional techniques such as extracorporeal shock wave lithotripsy, intraductal lithotripsy and/or stent placement. In non-operative patients in whom stone clearance cannot be achieved, long-term stent placement is a potential option in patients who are not candidates for further therapy. Endoscopic therapy may be effective in selected patients with intrahepatic biliary stones.