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When students answer test questions incorrectly, we often assume they don't understand the content; instead, they may struggle with certain cognitive skills or with how questions are asked. Our goal was to look beyond content to understand what makes assessment questions most challenging. On the basis of more than 76,000 answers to multiple-choice questions in a large, introductory biology course, we examined three question components—cognitive skills, procedural knowledge, and question forms—and their interactions. We found that the most challenging questions require the students to organize information and make meaning from it—skills that are essential in science. For example, some of the most challenging questions are presented as unstructured word problems and require interpretation; to answer correctly, the students must identify and extract the important information and construct their understanding from it. Our results highlight the importance of teaching students to organize and make meaning from the content we teach.