This study investigated questioning as practiced in Malaysian secondary school classrooms, to determine teachers' rationale for adopting certain techniques of questioning, and to use the findings to inform teacher education. Questioning is a central aspect of any classroom interaction as it serves so many functions but it is still an under-researched area in the Malaysian classroom context. This study employs an in-depth naturalistic approach and focuses on every day classroom events pertaining to questioning. Research constraints faced in conducting the fieldwork included dealing with the authorities, and the timing and duration of research as constrained by school schedules and national holidays presented by the multicultural milieu of Malaysia. It was found that the majority of questions set by EFL and science-as-content-taught-in-English classes were low-level and factual, and not designed to encourage critical thinking on the part of learners. There was a mismatch between what is stipulated by the national curriculum and how teachers actually teach in terms of posing questions. While national policy stipulates helping learners become critical thinkers, teachers seem concerned with other, short term goals. For instance, teachers' beliefs about their students' academic needs and what teachers should do in a classroom make them tailor their questions to align with the SPM examination (Malaysian Certificate of Education) with the result of posing more questions at a low-level factual category.