In this study, the perceptions of science classroom climate were investigated for 360 elementary and middle school students in mixed classes. The instrument used was an adapted version of the Student Perception Questionnaire (SPQ), which consists of five elements-Participatory Climate, Personalized Interaction, Student Assertiveness, Positive Teacher, and Negative Teacher. The results indicated that the gender differences in the perceptions of the Participatory Climate and the Positive Teacher were not significant for middle school students. However, the differences were found to be significant in the perceptions of the Negative Teacher, the Personalized Interaction and the Student Assertiveness, which measure the climate for the individual student. On the other hand, elementary male and female students did not significantly differ in the perceptions of science classroom climate except one item on the Participatory Climate. Educational implications are discussed.