Objectives As problem-based learning is increasingly used in medical education, there is a growing need to capture the diversity of the events occurring during problem-based learning sessions in order to understand the way in which students learn. The computer simulation described attempts to analyse a posteriori how students reason and learn during such sessions.Design A computer simulation was designed to perform a detailed analysis of the following features: pattern of information searched, formulation of working hypothesis and identi®cation of learning issues. The program, which has been running successfully for 2 years, was developed using local resources and accepts any clinical problem, provided it is written in a suitable text ®le format. The program has been applied in the discipline of pathophysiology.Setting Faculty of Medical Sciences of Lisbon, Portugal. Subjects Medical students.Results An example is presented of how prints were analysed in order to evaluate the`progression pro®le' of the students, and a comparison is made with other similar instruments.Conclusions The program improved understanding of the relationships between the inquiry strategy and hypothesis formulation and also of how self-learning (triggered by learning issues) in¯uenced further analysis of the cases.