Self-directed learning is believed to be an important aspect of the reflective clinical practitioner. This study was a comparison of student learning and student perceptions of course and instructor effectiveness, course difficulty, and amount learned between the active learning and lecture sections of a course. Participants in this study were 170 physical therapist students in 3 sections of a physiology course in the first year of their professional program. Course grades and the results of teacher-course evaluations were compared between a lecture section and an active learning section. The students in the original active learning section were reassessed 1 year later to determine their perceptions of the course. The differences were analyzed using Kruskal-Wallis and Mann-Whitney U tests. Course grades were higher in both active learning sections than in the lecture section. However, the students in both active learning sections perceived that they had learned less than students in the lecture section. Students' perceptions of course and instructor effectiveness were lower in the active learning sections than in the lecture section. There were no differences between the lecture and active learning sections on the students' perceptions of course difficulty. Although they did better in the active learning environment, physical therapist students in a basic sciences course (physiology) in the first year of their professional program perceived that they had learned less in active learning courses. They also had lower perceptions of course and instructor quality.