The objectives of this study were to (1) characterize the nature of biochemistry faculty members' "instructor thinking" with regard to teaching upper-level, large-lecture biochemistry courses, (2) identify factors associated with changes in instructor thinking, and (3) investigate the relationship between instructor thinking and teaching practice. For the purposes of this study, "instructor thinking" was defined as an instructor's thoughts about (1) teaching, including the role of instructors, student engagement, instructional strategies, and assessment and (2) students and learning, including personal experiences with learning, student roles and capabilities, and student learning. Instructor thinking of three university faculty members was investigated over the course of two semesters. Semi-structured in-depth interviews, faculty members' reflective journals, e-mail, course documents and investigator observations and field notes served as qualitative data sources. Descriptive and interpretive data coding methods were applied to the data and emergent themes were reported in three individual case studies depicting instructor thinking. A cross-case analysis of the three cases was conducted and revealed factors associated with changes in instructor thinking: pedagogical dissatisfaction, creation of productive spaces for reflection by a knowledgeable other, and experimentation with assessment strategies. These factors opened the door for new lines of instructor self-inquiry and introspection about teaching and, in some cases, created new prospects for change in teaching practice.