Spatial ability (SA) is the cognitive capacity to understand and mentally manipulate concepts of objects, remembering relationships among their parts and those of their surroundings. Spatial ability provides a learning advantage in science and may be useful in anatomy and technical skills in health care. This study aimed to assess the relationship between SA and anatomy scores in first- and second-year medical students. The training sessions focused on the analysis of the spatial component of objects' structure and their interaction as applied to medicine; SA was tested using the Visualization of Rotation (ROT) test. The intervention group (n=29) received training and their pre- and post-training scores for the SA tests were compared to a control group (n=75). Both groups improved their mean scores in the follow-up SA test (P<0.010). There was no significant difference in SA scores between the groups for either SA test (P=0.31, P=0.90). The SA scores for female students were significantly lower than for male students, both at baseline and follow-up (P<0.010). Anatomy training and assessment were administered by the anatomy department of the medical school, and examination scores were not significantly different between the two groups post-intervention (P=0.33). However, participants with scores in the bottom quartile for SA performed worse in the anatomy questions (P<0.001). Spatial awareness training did not improve SA or anatomy scores; however, SA may identify students who may benefit from additional academic support.