Endoscopic retrograde cholangiopancreatography (ERCP) in patients with Roux-en-Y anastomosis is a complex challenge. Long length of afferent limb after an acute angle at the jejunojejunostomy and altered location of the biliary orifice make biliary cannulation difficult. Single balloon enteroscopy assisted ERCP (SBE-ERCP) is a promising alternative to conventional approaches. The purpose of this study was to assess the efficacy and safety of SBE-ERCP in patients with Roux-en-Y reconstruction at a high volume tertiary referral center. This is a retrospective cohort study. All procedures were performed by a single, experienced pancreatobiliary endoscopist. Patient demographics and related clinical data were obtained. The rate of procedure successes and complications were determined. Fourteen patients (nine women) with a median age of 63years (range 35-83years) underwent 22 SBE-ERCP procedures from March 2009 to May 2011. Surgically altered anatomy consisted of Whipple procedure (n=4), hepaticojejunostomy (n=9) and partial gastrectomy (n=1). Indications for SBE-ERCP were obstructive jaundice (n=10), cholangitis (n=7), post-PTC internalization (n=3) and biliary stent extraction/exchange (n=2). The hepaticojejunostomy site (HJS) was reached in 15 (68%) procedures. Successful interventions were performed in 11 (73%) of 15 cases, including balloon dilation of biliary strictures (n=3), insertion of biliary stents (n=7), retrieval of biliopancreatic stents (n=4) and biliary stone extraction (n=4). The mean procedural time for successful interventions was 97.6min (range 73-147min). No procedural complications occurred during the median follow-up of 501days (range 22-1,242days). SBE-ERCP is safe and carries an acceptable success rate in experienced hands.