In the field of medical education, it is possible to consider that the acquisition of professional competences can gain new contours when considering the use of active methodologies. It is important to analyze the perception of the students about the use of them in medical courses, as well as to reflect on their challenges and potentials. In the present study, a semistructured questionnaire of student perception was applied immediately after the execution of different types of active methodologies in the discipline of physiology in two medical courses. The results suggest a highly positive evaluation of the use of active methodologies by the student body of the two institutions. The students evaluated positively the application of the method (94.6%) and the perception about the learning (84.1%). On the other hand, when questioned about the substitution of the traditional expository method by the active methodologies, there was a tendency to the centrality of the answers, with 84.0% of the responses concentrated at positions 2, 3, and 4 on a scale of 1 (minimum) to 5 (maximum) on the Likert scale. There were no statistically significant differences when comparing variables of age, sex, and previous graduation. Although there was no consensus regarding the full replacement of traditional for active methodologies, one can conclude that the students' perception about the introduction of said methodologies in the teaching of physiology in medical courses is positive, regardless of the subgroups evaluated. These results encourage the insertion of these and other methodologies into medical courses.