Magnetic resonance cholangiography (MRC) is an established diagnostic tool for noninvasive assessment of the biliary tract in humans. It has also been found to be feasible in companion animals, but no published studies have compared MRC sequences in veterinary medicine. The present study is part of a prospective, observational, analytical investigation on MR cholangiopancreatography performed on the donated bodies of 12 cats and eight dogs. The main aim of this study was to compare the images of 2D‐SSh‐TSE‐MRC and 3D‐TSE‐MRC sequences for visualization and image quality of the feline and canine biliary tract. Both sequences are T2‐weighted and noncontrast. Three independent readers scored the visibility of four segments of the biliary tract, namely the gallbladder (GB), cystic duct, common bile duct (CBD), and extrahepatic ducts, and the image quality of the two MRC sequences using five‐point Likert scales. Wilcoxon signed‐rank test was used to compare the scores between the MRC sequences separately for cats and dogs. Inter‐ and intraobserver agreements were measured using Gwet's AC2 with linear weighting. The 3D‐TSE‐MRC images were scored significantly higher than the 2D‐SSh‐TSE‐MRC for both visibility and image quality (P < .001–.016 for cats, P = .008–.031 for dogs); the only exception was GB in dogs. In both cats and dogs, interobserver agreement for segment visibility and image quality ranged from slight to substantial in 2D‐SSh‐TSE‐MRC and from poor to almost perfect in 3D‐TSE‐MRC. Most of the assessments (73% for segment visibility and 66% for image quality) had substantial to almost perfect intraobserver agreement. Findings from the current study support the use of 3D‐TSE‐MRC over 2D‐SSh‐TSE‐MRC for evaluation of the feline and canine biliary tract, but further studies on live animals are warranted.