Textbook anatomy depiction of the hepatobiliary tree is present in 55%-62% of the population. Misidentification of hepatobiliary variants can lead to bile duct injuries in cholecystectomies. A better understanding of variants has been cited as a key area for improvement in anatomy education. The aim of this study was to compare the effectiveness of 3D printed models with hepatobiliary variants to conventional 2D image-based teaching and assessment The study invited medical students to participate and were allocated to either a 2D image projection group or a 3D physical model group. Training sessions described arterial (5) and ductal (5) variant anatomy. While the 2D groups were taught with planar projections, the 3D group were taught variant anatomy using only 3D printed models. A multiple choice question form (with nine distractors per question) assessed identification of anatomical parts in both 2D images and tagged printed models for both groups. Thirty-four students participated in the study. The median total correct answer for 2D group was 83% (62%-94%) IQR, and 3D group was 83% (70%-94%) IQR. Both groups showed a significant increase in scores when assessed with 3D model, 2D and 3D groups (**p = 0.008, 0.003, respectively), two-tailed Wilcoxon-signed rank test. There was no difference in outcomes following two different methods of instruction (2D vs. 3D). However, both groups performed significantly better when tested on 3D models. This finding suggests that forms of assessment in anatomy may yield superior results when tailored to physical models.