Endoscopic management of bile duct stones is now the standard of care, but challenges remain with difficult bile duct stones. There are some known factors associated with technically difficult bile duct stones, such as large size and surgically altered anatomy. Endoscopic mechanical lithotripsy is now the standard technique used to remove large bile duct stones, but the efficacy of endoscopic papillary large balloon dilatation (EPLBD) and cholangioscopy with intraductal lithotripsy has been increasingly reported. In patients with surgically altered anatomy, biliary access before stone removal can be technically difficult. Endotherapy using two new endoscopes is now utilized in clinical practice: enteroscopyassisted endoscopic retrograde cholangiopancreatography and endoscopic ultrasound-guided antegrade treatment. These new approaches can be combined with EPLBD and/ or cholangioscopy to remove large bile duct stones from patients with surgically altered anatomy. Since various endoscopic procedures are now available, endoscopists should learn the indications, advantages and disadvantages of each technique for better management of bile duct stones.