Spatial abilities have been correlated to anatomy knowledge assessment and spatial training has been found to improve spatial abilities in previous systematic reviews. The objective of this systematic review was to evaluate spatial abilities training in anatomy education. A literature search was done from inception to 3 August 2017 in Scopus® and several databases on the EBSCOhost platform. Citations were reviewed and those involving anatomy education, an intervention, and a spatial abilities test were retained and the corresponding full-text articles were reviewed for inclusion. Before and after training studies, as well as comparative training programs, relating a spatial training intervention to spatial abilities were eligible. Of the 2,405 citations obtained, 52 articles were identified and reviewed, yielding eight eligible articles. Instruction in anatomy and mental rotations training were found to improve spatial abilities. For the seven studies retained for the meta-analysis that included the effect of interventions on spatial abilities test scores, the pooled treatment effect difference was 0.49 (95% CI [0.17; 0.82]; n = 11) improvement. For the two studies that included the practice effect on spatial abilities test scores in a control group, the pooled treatment effect difference was 0.47 (95% CI [-0.03; 0.97]; n = 2) improvement. In these two studies, the impact of the intervention on spatial abilities test scores was found despite the practice effect. Evidence was found for improvement of spatial abilities in anatomy education using instruction in anatomy and mental rotations training.