Currently, medical education context poses different challenges to anatomy, contributing to the introduction of new pedagogical approaches, such as computer-assisted learning (CAL). This approach provides insight into students' learning profiles and skills that enhance anatomy knowledge acquisition. To understand the influence of anatomy CAL on spatial abilities, a study was conducted. A total of 671 medical students attending Musculoskeletal (MA) and Cardiovascular Anatomy (CA) courses, were allocated to one of three groups (MA Group, CA Group, MA + CA Group). Students' pre-training and post-training spatial abilities were assessed through Mental Rotations Test (MRT), with scores ranging between 0-24. After CAL training sessions, students' spatial abilities performance improved (9.72 ± 4.79 vs. 17.05 ± 4.57, P < 0.001). Although male students in both MA Group and CA Group show better baseline spatial abilities, no sex differences were found after CAL training. The improvement in spatial abilities score between sessions (Delta MRT) was correlated with Musculoskeletal Anatomy training sessions in MA Group (r = 0.333, P < 0.001) and MA + CA Group (r = 0.342, P < 0.001), and with Cardiovascular Anatomy training sessions in CA Group (r = 0.461, P = 0.001) and MA + CA Group (r = 0.324, P = 0.001). Multiple linear regression models were used, considering the Delta MRT as dependent variable. An association of Delta MRT to the amount of CAL training and the baseline spatial abilities was observed. The results suggest that CAL training in anatomy has positive dose-dependent effect on spatial abilities.