Background: Fluoroscopy must be used cautiously during endoscopic retrograde cholangiopancreatography (ERCP). Radiation exposure data in patients with surgically altered anatomy undergoing enteroscopy-assisted ERCP (EA-ERCP) are scarce. Methods: 34 consecutive EA-ERCP procedures were compared with 68 conventional ERCP (C-ERCP) procedures. Patient and procedure characteristics and radiation data were collected. Results: Surgical reconstructions were gastrojejunostomy, Roux-en-Y hepaticojejunostomy, Roux-en-Y total gastrectomy, Roux-en-Y gastric bypass and Whipple’s duodenopancreatectomy. Procedures were restricted to biliary indications. Mean fluoroscopy time was comparable in both groups (370 ± 30 s EA-ERCP vs. 393 ± 40 s C-ERCP, p = 0.7074), whereas total mean radiation dose was lower in EA-ERCP (83 ± 6 mGy) compared to C-ERCP (110 ± 11 mGy, p = 0.0491) and dose area product (DAP) was higher in EA-ERCP (2216 ± 173 µGy*m2) compared to C-ERCP (1600 ± 117 µGy*m2, p = 0.0038), as was total procedure time (77 ± 5 min vs. 39 ± 3 min, p < 0.0001). Enteroscope insertion to reach the bile duct during EA-ERCP took 28 ± 4 min, ranging from 4 to 90 min. These results indicate that C-ERCP procedures are generally more complex, needing magnified fluoroscopy, whereas EA-ERCP procedures take more time for enteroscope insertion under wide field fluoroscopic guidance (increased DAP) with less complex ERCP manipulation (lower total radiation dose). Conclusions: Radiation exposure during EA-ERCP in surgically altered anatomy is different as compared to C-ERCP. EA-ERCP takes longer with a higher DAP because of the enteroscope insertion, but with lower total radiation dose because these ERCP procedures are usually less complex.