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Learning cardiac morphology largely involves spatial abilities and studies indicate benefits from innovative 3D visualization technologies that speed up and increase the learning output. Studies comparing these teaching tools and their educational output are rare and few studies include complex congenital heart defects. This study compared the effects of 3D prints, mixed reality (MR) viewing of 3D meshes and standard cardiac CT slice images on medical students' understanding of complex congenital heart defect morphology, measuring both objective level of understanding and subjective educational experience. The objective of this study was to compare morphological understanding and user experiences of 3D printed models, MR 3D visualization and axial 2D CT slices, in medical students examining morphological details in complex congenital heart defects. Medical students in the median 4th year of study (range 2nd to 6th) examined three of five different complex congenital heart defects by three different modalities: 3D printed model, MR viewed 3D mesh, and cardiac CT slices, answering a questionnaire on morphology and user experience. Time to complete task, diagnostic accuracy, and user experience data were collected and compared on group level. Task times were similar for all modalities. The percentage of correct answers was higher with MR visualization, which was also the preferred modality overall. Medical students both prefer and better understand the morphology of complex congenital heart disease with 3D models viewed using MR, without spending more time than with 3D prints or 2D CT images.