Critical thinking skills are crucial for success in the modern workforce, particularly for graduate students, who often aim to become physicians or researchers. Primary literature provides an excellent opportunity to practice these skills. We describe a course that includes a structured analysis of four recent papers from diverse fields of biology. To facilitate a critical approach to primary literature, we included a paper with questionable data interpretation and two papers investigating the same biological question, yet reaching opposite conclusions. We report a significant increase in students' self‐efficacy in analyzing data from research papers, evaluating authors' conclusions, and designing experiments. However, using our critical thinking skills test, we observed a statistically significant increase in students' performance in experimental design, but not in analysis or evaluation. Our analysis of students' responses to the question: “What aspects of reading and analyzing primary literature do you find most challenging?” revealed post‐instructional changes in students' perceptions. After instruction, we observed a shift in the cognitive level of challenges our students associated with primary literature, from Lower Order to Higher Order Cognitive Skills. These changes are also consistent with the transition from a novice to a competent reader.