This article presents the results of a study that examined students’ ability to retain what they have learned in an anatomy course after thirty days via using various learning tools for twenty minutes. Fifty-two second-year medical students were randomly assigned to three learning tools: text-only, three-dimension visualisation in a two-dimensional screen (3DM), or mixed reality (MR). An anatomy test lasting for twenty minutes measuring spatial and nominal knowledge was taken immediately after the learning intervention and another thirty days later. Psychometric tests were also used to measure participants’ memory, reasoning and concentration abilities. Additionally, electroencephalogram data was captured to measure the participants’ awakeness during the learning session. Results of this study showed that the MR group performed poorly in the nominal questions compared to the other groups; however, the MR group demonstrated higher retention in both the nominal and spatial type information for at least a month compared to the other groups. Furthermore, participants in the 3DM and MR groups reported increased engagement. The results of this study suggest that three-dimensional visualiser tools are likely to enhance learning in anatomy education. However, the study itself has several limitations; some include limited sample size and various threats to internal validity.