Every classroom constructs its own culture through the interactions of all participants, students and instructors. This culture, often covert or invisible, has a direct impact on students’ opportunities to learn. Therefore, it is critical that instructors understand their classrooms’ interaction patterns and their effect on student learning. We suggest that discourse analysis may serve as a tool to enhance instructors’ understanding of their classrooms and to serve as an intervention particularly useful for junior faculty as they are beginning their teaching career. To this end, this paper (1) describes the theoretical foundation of discourse analysis and (2) demonstrates its application, effectiveness, and applicability in STEM classrooms, particularly at the introductory level, the time when students make their first steps in negotiating ‘academic literacies’.