Background: Endoscopic retrograde cholangiopancreatography is an established therapeutic modality for pancreaticobiliary disease. Congenital anatomical anomalies, including situs inversus totalis and rare hepatobiliary malformations, substantially increase the technical complexity of endoscopic retrograde cholangiopancreatography and are seldom encountered in clinical practice. Published experience is limited predominantly to individual case reports and smaller case series. Methods: We present a report of three patients who underwent endoscopic retrograde cholangiopancreatography: two with situs inversus totalis and choledocholithiasis complicated by acute cholangitis, and one with a rare congenital anomaly consisting of a completely separated right hepatic lobe combined with choledocholithiasis. Results: Successful endoscopic retrograde cholangiopancreatography was achieved in all three patients. In both situs inversus totalis cases, biliary cannulation and stone clearance were accomplished using modified endoscopic techniques, including endoscope rotation and positional adjustments, without procedural complications. In the patient with the separated hepatic lobe, endoscopic retrograde cholangiopancreatography allowed common bile duct stone clearance; however, an attempted mechanical lithotripsy of a gallbladder calculus resulted in basket entrapment, necessitating surgical treatment. Conclusions: Endoscopic retrograde cholangiopancreatography is feasible and effective in patients with congenital hepatobiliary anomalies, but demands meticulous pre-procedural planning, thorough anatomical understanding, and technical versatility. A cautious step-by-step approach and readiness to adapt technique are essential to optimise outcomes and minimise risk.