BACKGROUND Retrograde cholangiopancreatography using double-balloon endoscopic retrograde cholangiography (DBERC) is a valuable technique to treat biliary stone and jejunobiliary anastomotic stenosis in patients with altered gastrointestinal anatomy. The accurate selection of the route at the anastomosis branch is one of the most important factors in reaching the target in a timely manner. AIM To determine the accuracy of carbon dioxide insufflation enterography (CDE) at the branch for selecting the correct route during DBERC. METHODS We enrolled 52 consecutive patients scheduled for DBERC at our institution from June 2015 to November 2017. Route selection via two methods (visual observation and CDE) was performed in each patient. We determined the correct rate of route selection using CDE. RESULTS Thirty-three patients had a jejunojejunal anastomosis and 19 patients had a gastrojejunal anastomosis. The therapeutic target region was reached in 50 patients. The mean procedure times from the teeth to the target (total insertion time), from the teeth to the branch, and from the branch to the target, and the mean total examination time were 15.2, 5.0, 8.2, and 60.3 min, respectively. The rate of correct route selection using visual observation and CDE were 36/52 (69.2%) and 48/52 (92.3%), respectively (P = 0.002). The rate of correct route selection using CDE in patients with a jejunojejunal anastomosis was 29/33 (87.8%), and the rate in patients with a gastrojejunal anastomosis was 19/19 (100%). CONCLUSION CDE is helpful in selecting the route at the branch in the anastomosis for more timely access to the target in patients with altered gastrointestinal anatomy undergoing DBERC.