We have adapted the Structure of Observed Learning Outcomes (SOLO) taxonomy for evaluating student learning in a two-semester organic chemistry course sequence. The SOLO taxonomy describes student learning in five hierarchical levels related to the student’s ability to apply appropriate concepts in answering questions, connect concepts together coherently, and relate concepts to new ideas. Student responses to open-ended questions that show no relevant processing of information are ranked as Prestructural; those that show only preliminary processing rank as Unistructural. In Multistructural responses, students address some aspect of the question but are unable to relate ideas. Preferred levels of understanding are those demonstrated when students integrate several aspects of the question to produce coherent meaning (ranked as Relational) or generalize to a higher level of abstraction (called Extended Abstract). We found this method to be a powerful tool to analyze points of difficulty or confusion in student learning and helpful in following the progress in students’ conceptual understanding.