Researchers observed 28 university faculty in graduate and undergraduate science and mathematics courses in a three-year, longitudinal study of teaching. Subjects were selected from five higher education institutions in the state where faculty had a two- to five-year association with a reform-based NSF professional development program. Observer field notes and a researcher-designed observation instrument were used to describe and compare teaching practices. The participants in this study taught science and mathematics content courses for majors, non-majors, as well as education majors. Our observation method created a descriptive profile that enabled comparisons across a variety of teaching contexts. The main results showed that the faculty lacked practices that supported development of divergent thinking, conceptual thinking, and metacognitive thinking skills. Observed differences in the profiles of instruction included greater emphasis on real-world connections in science and greater use of cooperative problem solving in mathematics. A case study of a large lecture course describes reformed teaching practices in even the most challenging setting.