An inquiry-oriented laboratory in chemistry was integrated into the chemistry curriculum in Jewish high schools in Israel, and after a short period was also implemented in Arab sector. In this study, we investigated the effect of culture on the perceptions of laboratory classroom learning environments by comparing the perceptions of Arab and Jewish high school students who learned the inquiry-oriented chemistry laboratory. The learning environment is influenced by student-teacher relationship and we thought that this relation is an important issue in the inquiry laboratory and is different between the Arab and Jewish populations. However, until recently, the Arab teachers have remained in the centre of the learning process and their students perceived them as the main source of knowledge and information. In this study, we used both quantitative and qualitative methods to determine whether the laboratory learning environment was different in Arab and Jewish classes that learned in the inquiry-oriented laboratory in chemistry. A statistical comparison of Arab and Jewish inquiry groups revealed significant differences in their actual and preferred perceptions. From the qualitative part of the study, we found that the teachers and students from the Arab and Jewish sectors were statistically similar in the categories that we measured during the inquiry phase, but they were statistically different during the pre-inquiry phase of the laboratory. From the interviews with the teachers and the students, we found that there were differences in the student-teacher relationship between the two sectors.