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Students often experience difficulty in interpreting conventional textbook images [1,2]. One of the most challenging topics in veterinary anatomy is to identify the correct structures of skulls in different species. The aim of the study was to examine the impact of 3D scans on students’ learning process compared to traditional 2D images. For this purpose, annotated 3D scans of horse and pig skulls were generated and made available on Sketchfab. During practical classes a total of 118 second-year students were divided into three groups, which received different learning materials (3D scans, 2D images annotated with arrows or with numbers). The anatomical knowledge of students was tested using an objective structured practical examination before and after the learning session. In addition, spatial ability was tested using the mental rotation test. After the study, the students could provide feedback on quality and usability of the different learning tools. All groups showed significantly improved results in the post-test compared to the pre-test. The 3D scans group scored the best, followed by the 2D arrows group and then by the 2D numbers group. However, results between the groups did not differ significantly from each other. The results of the mental rotation test were positively correlated with the results of the 3D scans and the 2D arrows group, but negatively correlated with the results of the 2D numbers group. The survey of the students revealed that they perceived 3D scans as beneficial learning material. They also indicated a great interest in this alternative learning material. These data suggest that 3D scans could be useful as an alternative learning material to ease the learning process and improve motivation of students, even though they do not necessarily contribute to a better learning outcome than 2D images.