Bile duct stones in patients with surgically altered anatomy still pose a challenge to endoscopists. For successful endoscopic management of bile duct stones, there are multiple hurdles: Intubation to the afferent limb, biliary cannulation, ampullary intervention and stone extraction. The major advancement in this area is the development of dedicated device-assisted endoscopes for endoscopic retrograde cholangiopancreatography (ERCP). In patients with Billroth II reconstruction, a high technical success rate is reported using a duodenoscope but can be complicated by a potentially high perforation rate. In patients with Roux-en-Y reconstruction, device-assisted ERCP shows high technical success and low adverse event rates. Meanwhile, endoscopic papillary large balloon dilation enables safe and effective stone extraction with less use of endoscopic mechanical lithotripsy in patients with a dilated distal bile duct, but intraductal lithotripsy is sometimes necessary for management of very large bile duct stones. In cases with difficult stones, alternative approaches such as laparoscopy-assisted ERCP and endoscopic ultrasound (EUS)-guided intervention are increasingly reported with preliminary but promising results. However, comparative studies are still lacking in this area and prospective randomized controlled trials are warranted in terms of safety, efficacy and cost-effectiveness.