Science faculty who want to improve instructional strategies need to design appropriate methods for assessing and analyzing classroom data to determine the effectiveness of their approaches to learning. We used systematic strategies derived from methods of discipline-based science research to design problems to assess students' understanding of the carbon cycle in two introductory biology courses for science majors. Among typical misconceptions are the ideas that gaseous carbon dioxide is not respired during decomposition by organisms in the soil and that plants acquire carbon from the soil rather than from the air through leaves during photosynthesis. Diagnostic problems provided data on students' understanding and misconceptions. In-class instruction, problems, and laboratories were designed to focus on student misconceptions and provided formative assessment. After two semesters, results indicated that the majority of students responded accurately; however, 20 to 40 percent of the students maintained misconceptions even after instruction. Assessment strategies enabled us to collect, analyze, and report data that will influence future instruction.