Students often struggle with interpreting traditional textbook images and translating them to anatomical structures. This study aimed to compare the impact of 3D scans versus 2D images on students' learning outcomes when learning anatomical structures on skulls from horses and pigs. Furthermore, the correlation between spatial ability and learning outcomes using 3D scans or 2D images was examined. Second-year veterinary medicine students either used 3D scans or 2D images, annotated with arrows or numbers as learning material. Students' anatomical knowledge was tested before and after the learning session, and spatial ability was assessed using the mental rotation test. All groups improved significantly in the post-test. However, the differences between groups were not significant, suggesting that 3D scans do not necessarily lead to higher learning outcomes. The analysis of the correlation between spatial ability and learning outcomes did not prove that students with weaker spatial ability benefit from 3D scans. Students preferred 3D scans over 2D images despite similar outcomes, suggesting they are valuable for learning. However, results show that the introduction of novel learning materials likely amplified the impact of reduced learning time on the 3D group, as these materials necessitated additional time for effective comprehension and integration.