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In this article we present a comparative study in which we analyzed teacher questions in two different languages of instruction, namely, English‐medium instruction (EMI) and Basque‐medium instruction (BMI) classes at university. For this purpose, we videotaped and analyzed two teachers who delivered 29 lessons forming a corpus of 39 h of recording. The tool used for classroom observations and for the analysis was the Communicative Orientation of Language Teaching observation scheme, which was then followed by statistical analyses. Results revealed that the language of instruction did not exert an influence on questioning practices, since there were no significant differences between EMI and BMI lessons. However, results revealed teachers and their teaching style as an influential variable when it came to questioning. In both languages the most utilized types of questions were Display Questions, followed by Convergent Referential Questions, which indicated that lower‐order questions predominated over higher‐order questions. As for pedagogical implications, we highlight the need for teacher training so that lecturers become aware of the importance of promoting interaction in the classroom through questions, as well as the positive impact of asking higher‐order questions that entail a cognitive challenge for the students.