Peer instruction has been used extensively in lecture courses; however, there is little evidence of its use in laboratory courses. The purpose of the present study was to describe the implementation of the peer instruction method in a physiology laboratory course in China. Second-year medical students attended a 6-wk physiology laboratory course in the fall semester of the 2016-2017 school year. In the six new physiology laboratory classes, peer instruction strategies were used to substitute for the traditional short, didactic lectures. The effects of peer instruction were measured by in-class quizzes and confidence levels. The students' evaluations of peer instruction were measured by a Likert scale questionnaire. Peer instruction significantly improved the mean score on quizzes (0.53 [plus or minus] 0.50 vs. 0.68 [plus or minus] 0.47, P [less than] 0.001) and confidence levels (2.36 [plus or minus] 0.66 vs. 2.80 [plus or minus] 0.45, P [less than] 0.001). Furthermore, for individual incorrect answers, 39.07% changed to correct answers after peer instruction, whereas, for correct answers, 6.61% were changed to an incorrect response. Overall, significantly more students changed their answers from incorrect to correct than from correct to incorrect [X[superscript 2] : 333.11; degrees of freedom (df): 1; P [less than] 0.001]. Therefore, the positive effects of peer instruction were higher than the negative effects (X[superscript 2] : 244.55; df: 1; P [less than] 0.001). Moreover, student evaluations of peer instruction were highly positive. In conclusion, the implementation of peer instruction to the physiology laboratory course is an effective strategy to enhance students' performance on in-class quizzes and confidence levels. In addition, the attitude of students toward peer instruction was favorable.