The aim of this study was to evaluate where magnetic resonance (MR) cholangiography can accurately demonstrate the presence, extent, and type of choledochal cysts. Eight patients with sonographically suspected choledochal cysts were evaluated with 2D and 3D FASE MR cholangiography technique. The presence, extent, and type of choledochal cyst were determined. MR cholangiographic findings were correlated with the gold standard of endoscopic retrograde cholangiography and surgery in all patients, with CN in five. All MR cholangiograms were correlated with findings at surgery, endoscopic retrograde cholangiography or CT. There were six Todani type I and one Todani type IV choledochal cysts. The extent of involvement was correctly demonstrated on all MR cholangiograms. Calculi and sludge were correctly identified on the MR cross-sectional images in four patients but were not seen on MR cholangiograms in one. In one patient with an initially misinterpreted choledochal cyst, MR sectional images showed the typical appearance of a hydatid cyst, which was confirmed at surgery. MR cholangiography can be used to confirm the diagnosis of choledochal cysts and define the extent of involvement preoperatively. Non-biliary cysts such as a hydatid cyst can mimic a choledochal cyst on the MR cholangiogram and should be correlated with the MR cross-sectional images to avoid misinterpretation.