This study reports cross-validation results for an Indonesian-language version of a modified form of the What Is Happening In this Class? (WIHIC) questionnaire and its use in investigating the nature of science classroom learning environments in Indonesian lower secondary schools. Following administration of the WIHIC to approximately 1400 students and their teachers in 16 schools, the study led to five assertions. First, the study confirmed that the Indonesian version of the modified WIHIC is a valid and reliable instrument for measuring the classroom learning environment in the Indonesian educational context. Second, there were significant differences between students' perceptions of the actual and preferred learning environment, with students tending to prefer a more favourable classroom learning environment than the one which they actually experienced. Third, female students generally held slightly more positive perceptions of both actual and preferred learning environments. Fourth, students held less favourable perceptions of both actual and preferred learning environments than did their teachers. Finally, there were significant differences in students' perceptions of the actual classroom learning environment depending on the schools' locality, with students in rural schools holding less favourable perceptions than students in urban and suburban schools for all seven WIHIC scales. Students in urban and suburban schools perceived their classroom environments similarly with the exception that students in urban schools perceived greater cooperation and less teacher support than did students in suburban schools.