A detailed understanding of the cognitive process underlying diagnostic reasoning in medical experts is currently lacking. While high-level theories like hypothetico-deductive reasoning were proposed long ago, the inner workings of the step-by-step dynamics within the mind remain unknown. We present a fully automated approach to elicit, monitor, and record diagnostic reasoning processes at a fine-grained level. A web-based user interface enables physicians to carry out a full diagnosis process on a simulated patient, given as a pre-defined clinical vignette. By collecting the physician's information queries and hypothesis revisions, highly detailed diagnostic reasoning trajectories are captured leading to a diagnosis and its justification. Four expert epileptologists with a mean experience of 19 years were recruited to evaluate the system and share their impressions in semi-structured interviews. We find that the recorded trajectories validate proposed theories on broader diagnostic reasoning, while also providing valuable additional details extending previous findings.