Medical school assessments should foster the development of higher-order thinking skills to support clinical reasoning and a solid foundation of knowledge. Multiple-choice questions (MCQs) are commonly used to assess student learning, and well-written MCQs can support learner engagement in higher levels of cognitive reasoning such as application or synthesis of knowledge. Bloom’s taxonomy has been used to identify MCQs that assess students’ critical thinking skills, with evidence suggesting that higher-order MCQs support a deeper conceptual understanding of scientific process skills. Similarly, clinical practice also requires learners to develop higher-order thinking skills that include all of Bloom’s levels. Faculty question writers and examinees may approach the same material differently based on varying levels of knowledge and expertise, and these differences can influence the cognitive levels being measured by MCQs. Consequently, faculty question writers may perceive that certain MCQs require higher-order thinking skills to process the question, whereas examinees may only need to employ lower-order thinking skills to render a correct response. Likewise, seemingly lower-order questions may actually require higher-order thinking skills to respond correctly. In this Perspective, the authors describe some of the cognitive processes examinees use to respond to MCQs. The authors propose that various factors affect both the question writer and examinee’s interaction with test material and subsequent cognitive processes necessary to answer a question.