ABSTRACT Objective to evaluate the effectiveness of the 3D virtual anatomical table as a complementary resource to the learning of the hepatobiliary anatomy by undergraduate medical students. Method A randomized controlled study comparing the anatomical learning of hepatobiliary structures, supported by a real model versus a virtual model, both three-dimensional (3D), by undergraduate medical students. The students’ perception of the resources used to teach anatomy was also evaluated. The students were submitted to a pre-test and to two evaluations after the interventions were applied. Results Overall, both the 3D virtual anatomical table and the real liver increased students’ knowledge of the hepatobiliary anatomy in relation to their previous knowledge (p = 0.001 and p = 0.01, respectively for second and third evaluations). In the longitudinal comparison between the pre-test and the second evaluation (hepatobiliary anatomy and Couinaud’s segmentation), this increase was significantly higher in the group allocated to the real liver (p = 0.002); in the comparison of the pre-test with the third evaluation (inclusion of adjacent organs in the anatomical table or in the real liver), the increase in knowledge was significantly higher in the group allocated to the anatomical table (p = 0.04). The perception of participants’ satisfaction regarding the learning resources was considered very good, with a minimum percentage of satisfaction of 80%. Conclusion the 3D virtual anatomical table provided more hepatobiliary anatomy knowledge than a real liver for undergraduate medical students, in comparison to their previous knowledge about these structures. In the cross-sectional comparison of the post-instruction evaluations, there was no difference between the two interventions. Moreover, the 3D platform had a positive impact on the level of satisfaction of study participants. This study shows that the 3D virtual anatomical table has the potential to improve both medical students’ understanding and interest in anatomy. It is recommended, however, that future protocols such as this be carried out with larger samples and exploring other anatomical structures.