In response to empirical evidence and calls for change, individual undergraduate biology instructors are reforming their pedagogical practices. To assess the effectiveness of these reforms, many instructors use course-specific or skill-specific assessments (e.g., concept inventories). We commend our colleagues' noble efforts, yet we contend that this is only a starting point. In this Perspectives article, we argue that departments need to engage in reform and programmatic assessment to produce graduates who have both subject-matter knowledge and higher-order cognitive skills. We encourage biology education researchers to work collaboratively with content specialists to develop program-level assessments aimed at measuring students' conceptual understanding and higher-order cognitive skills, and we encourage departments to develop longitudinal plans for monitoring their students' development of these skills.