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It is not known whether initial endoscopic ultrasonography (EUS) or magnetic resonance cholangiopancreatography (MRCP) is more cost effective than endoscopic retrograde cholangiopancreatography (ERCP).A cost-effectiveness analysis of EUS, MRCP and ERCP was performed on 163 patients. The effectiveness of an investigation was defined as the percentage of patients with no need for further evaluation after the investigation in question had been performed. Costs were assumed from the budget-holder's point of view.MRCP, EUS and ERCP had a total accuracy of 0.91, 0.93 and 0.92, respectively. Eighty-four (52%) patients needed endoscopic therapy in combination with ERCP, giving an effectiveness of MRCP, EUS, and ERCP of 0.44, 0.45 and 0.92, respectively. The cost-effectiveness of MRCP, EUS, and ERCP was 6622, 7353 and 4246 Danish Kroner (DKK) per fully investigated and treated patient (1 DKK = 0.14 EUR).Within a patient population with a probability of therapeutic ERCP in 50% of the patients, ERCP was the most cost-effective strategy.