Laboratory practices facilitate deep learning in biomedical sciences, however, they require experience in laboratory techniques, financial resources and institutional infrastructure. This is why the use of “in silico” or virtual laboratories is a viable alternative to teach fundamental biomedical concepts to students of medicine and science. Our objective is to evaluate the impact of virtual laboratories on medical students. Students of the third and fourth semesters of medicine used simvesel and simheart (Virtual Phisiology) simulators. We evaluated the perceptions and outcomes associated with the simulation of experiments related to concepts of the autonomic nervous system and cardiac mechanics. Students from earlier semesters arrive with less prior knowledge than advanced students. However, both groups improve their mastery of the subject in similar magnitude. Although the instructions and tasks were the same for the groups, the students of third semester seem to have more problems with the manipulation of the simulator and show a slightly less positive experience. After a second experience with the simulator, advanced students do not show changes in their already positive experience with the simulator. Third semester students, however, report a much higher functionality and usability with the simulator and a more favorable impact on their learning. In conclusion, the use of virtual laboratories is a cost‐effective intervention to teach complex concepts of physiology and pharmacology. Students consider that these types of laboratories allow them to achieve deeper learning even though they may need to gain mastery in some elements of the simulators. Teachers should consider the importance of the students' experience when developing biomedical simulation activities. Support or Funding Information Universidad de los Andes, Medical School and “Innovations in Education” Initiative of Conecta‐Te. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .