To promote higher-order thinking in college students, we undertook an effort to learn how to assess critical-thinking skills in an introductory biology course. Using Bloom's taxonomy of educational objectives to define critical thinking, we developed a process by which (a) questions are prepared with both content and critical-thinking skills in mind, and (b) grading rubrics are prepared in advance that specify how to evaluate both the content and critical-thinking aspects of an answer. Using this methodology has clarified the course goals (for us and the students), improved student metacognition, and exposed student misconceptions about course content. We describe the rationale for our process, give detailed examples of the assessment method, and elaborate on the advantages of assessing students in this manner.