In patients with Roux-en-Y (R-Y) anastomosis (including hepaticojejunostomy and R-Y gastric bypass) and Whipple operation, endoscopic retrograde cholangiopancreatography (ERCP) can be challenging. We retrospective analyses our experience with ERCP using balloon-assisted enteroscopy (BAE) (BAE-ERCP) in patients with R-Y anastomosis and Whipple operation.ERCP was performed in 15 patients (4 pancreaticoduodenectomy and 10cholangiojejunostomy and 1 Subtotal gastrectomy with R-Y reconstruction; age ranging from 4 to 63 years) with BAE. Double- and single-balloon enteroscopy was applied in 5 and 10 patients, respectively.Bile duct cannulation was successful in 13 of 15 cases (86.7%), including simple stenosis of the anastomotic stoma (n = 2), intrahepatic bile duct stones (n = 10), and pancreatic cancer (n = 1). Cannulation failed because the guidewire could not pass through the anastomotic stenosis in 1 patient and because the endoscope could not enter the acute angle of the anastomosis of the afferent limb in the other patient. Adverse events included jaundice (n = 1) and perforation (n = 1), which were successfully treated by conservative therapy.ERCP with BAE in patients with R-Y anastomosis and Whipple operation is safe and useful but has unique complications. The success rate is lower than that of conventional ERCP.