OBJECTIVE: To explore the diagnostic thinking process of medical students. SUBJECTS AND METHODS: Two hundred twenty-four medical students were presented with 3 clinical scenarios corresponding to high, low, and intermediate pre-test probability of coronary artery disease. Estimates of test characteristics of the exercise stress test, and pre-test and post-test probability for each scenario were elicited from the students (intuitive estimates) and from the literature (reference estimates). Post-test probabilities were calculated using Bayes' theorem based upon the intuitive estimates (Bayesian estimates of post-test probability) and upon the reference estimates (reference estimates of post-test probability). The differences between the reference estimates and the intuitive estimates, and between Bayesian estimates and the intuitive estimates were used for assessing knowledge of test characteristics, and ability of estimating pre-test and post-test probability of disease. RESULTS: Medical students could not rule out disease in low or intermediate pre-test probability settings, mainly because of poor pre-test estimates of disease probability. They were also easily confused by test results that differed from their anticipated results, probably because of their inaptitude in applying Bayes' theorem to real clinical situations. These diagnostic thinking patterns account for medical students or novice physicians repeating unnecessary examinations. CONCLUSIONS: Medical students' diagnostic ability may be enhanced by the following educational strategies: 1) emphasizing the importance of ruling out disease in clinical practice, 2) training in the estimation of pre-test disease probability based upon history and physical examination, and 3) incorporation of the Bayesian probabilistic thinking and its application to real clinical situations.