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The aim of the study was to compare prospectively magnetic resonance cholangiography (MRC) and magnetic resonance imaging (MRI) with endoscopic retrograde cholangiography (ERC) in the diagnosis and staging of Klatskin tumours of the biliary tree (hilar cholangiocarcinomas). Forty-six patients with suspected Klatskin tumours of the biliary tract underwent MRI and heavily T2-weighted, non-breathhold, respiratory-triggered fast spin-echo MRC. Forty-two patients underwent ERC within 24 h; in four patients, ERC was not feasible, and percutaneous trans-hepatic cholangiography (PTC) was carried out instead. Two independent investigators evaluated imaging results for the presence of tumour, bile duct dilatation, and stenosis. Clinical and histopathological correlation revealed Klatskin tumours in 33 patients. MRI revealed a slightly hyperintense signal of infiltrated bile ducts in T2-weighted fast spin-echo sequences. The malignant lesion was regularly visualized as a hypointense area in T1-weighted gradient-echo sequences with substantial contrast enhancement along the involved bile duct walls. MRC revealed the location and extension of the tumour in 31 of 33 cases correctly (sensitivity 94%, specificity 100%, diagnostic accuracy 95%). In 27 of 31 cases, ERC enabled accurate staging and diagnosis of Klatskin tumours with a sensitivity of 87%. ERC and PTC combined yielded a sensitivity of 84% and a specificity of 97%. Tumours were grouped according to the Bismuth classification, with MRC allowing correct identification of type I tumour in seven patients, type II tumour in four patients, type III tumour in 12 patients, and type IV tumour in ten patients. MRC provided superior visualization of completely obstructed peripheral systems. MRC in combination with MRI is a reliable non-invasive diagnostic method for the pre-therapeutic staging of Klatskin tumours.