We tested the hypothesis that peer instruction enhances student performance on qualitative problem-solving questions. To test this hypothesis, qualitative problems were included in a peer instruction format during our Physiology course. Each class of 90 min was divided into four to six short segments of 15 to 20 min each. Each short segment was followed by a qualitative problem-solving scenario that could be answered with a multiple-choice quiz. All students were allowed 1 min to think and to record their answers. Subsequently, students were allowed 1 min to discuss their answers with classmates. Students were then allowed to change their first answer if desired, and both answers were recorded. Finally, the instructor and students discussed the answer. Peer instruction significantly improved student performance on qualitative problem-solving questions (59.3 ± 0.5% vs. 80.3 ± 0.4%). Furthermore, after peer instruction, only 6.5% of the students changed their correct response to an incorrect response; however, 56.8% of students changed their incorrect response to a correct response. Therefore, students with incorrect responses changed their answers more often than students with correct responses. In conclusion, pausing four to six times during a 90-min class to allow peer instruction enhanced student performance on qualitative problem-solving questions.