Introduction: The use of new technologies is a new concept that facilitates learning. Objective: To evaluate the use of new technologies as a virtual instrument in the learning of the cardiac anatomy and to evaluate its impact on learning. Materials and methods: Dissection of human heart, vascular repletion, photographic record and subsequent software development by professional in Mechatronics Engineering. An experimental study was carried out, where two groups were randomly chosen from the Medicine program, one control and the other a study, made up of 40 students each. Both groups received lectures and practices in the amphitheater, that is, the traditional methodology. The control group followed the traditional methodology, being instructed of atlas texts of anatomy. The study group was further instructed by applying 3D Heart-tomy software in computer rooms, a three-dimensional virtual instrument. Results: Theoretical, practical and an opinion surveys were analyzed, finding that students in the study group obtained a better academic performance in the theoretical evaluation than the control group. Conclusion: Virtual media in 3D facilitates the understanding of the location of the structure, works as a pedagogical tool, but does not replace the practices in the amphitheater.