Visual-spatial abilities are considered a successful predictor in anatomy learning. Previous research suggest that visual-spatial abilities can be trained, and the magnitude of improvement can be affected by initial levels of spatial skills. This case-control study aimed to evaluate (1) the impact of an extra-curricular anatomy dissection course on visual-spatial abilities of medical undergraduates and (2) the magnitude of improvement in students with initially lower levels of visual-spatial abilities, and (3) whether the choice for the course was related to visual-spatial abilities. Course participants (n = 45) and controls (n = 65) were first and second-year medical undergraduates who performed a Mental Rotations Test (MRT) before and 10 weeks after the course. At baseline, there was no significant difference in MRT scores between course participants and controls. At the end of the course, participants achieved a greater improvement than controls (first-year: [Delta]6.0 ± 4.1 vs. [Delta]4.9 ± 3.2; ANCOVA, "P" = 0.019, Cohen's "d" = 0.41; second-year: [Delta]6.5 ± 3.3 vs. [Delta]6.1 ± 4.0; "P" = 0.03, Cohen's "d" = 0.11). Individuals with initially lower scores on the MRT pretest showed the largest improvement ([Delta]8.4 ± 2.3 vs. [Delta]6.8 ± 2.8; "P" = 0.011, Cohen's "d" = 0.61). In summary, (1) an anatomy dissection course improved visual-spatial abilities of medical undergraduates; (2) a substantial improvement was observed in individuals with initially lower scores on the visual-spatial abilities test indicating a different trajectory of improvement; (3) students' preferences for attending extracurricular anatomy dissection course was not driven by visual-spatial abilities.