Background: Patients with biliary obstruction are at high risk to develop septic complications after endoscopic retrograde cholangiography (ERC). We evaluated the benefits of local application of antimicrobial agents into ERC contrast media in preventing post-ERC infectious complications in a high-risk study population. Methods: Patients undergoing ERC at our tertiary referral center were retrospectively included. Addition of vancomycin, gentamicin and fluconazol into ERC contrast media was evaluated in a case-control design. Outcomes comprised infectious complications within 3 days after ERC. Results: In total, 84 ERC cases were analyzed. Primarily indications for ERC were sclerosing cholangitis (75%) and malignant stenosis (9.5%). Microbial testing of collected bile fluid in the treatment group was positive in 91.4%. Detected organisms were sensitive to the administered antimicrobials in 93%. The use of antimicrobials in contrast media was associated with a significant decrease in post-ERC infectious complications compared to non-use (14.3% vs. 33.3%; odds ratio [OR]: 0.33, 95% confidence interval [CI]: 0.114-0.978). After adjusting for the variables acute cholangitis prior to ERC and incomplete biliary drainage, the beneficial effect of intraductal antibiotic prophylaxis was even more evident (OR = 0.153; 95% CI: 0.039-0.598, p = 0.007). Patients profiting most obviously from intraductal antimicrobials were those with secondary sclerosing cholangitis. Conclusion: Local application of a combination of antibiotic and antimycotic agents to ERC contrast media efficiently reduced post-ERC infectious events in patients with biliary obstruction. This is the first study that evaluates ERC-related infectious complications in patients with secondary sclerosing cholangitis. Our first clinical results should now be prospectively evaluated in a larger patient cohort to improve the safety of ERC, especially in patients with secondary sclerosing cholangitis.