The aim of the study is to show the application of the case method for studying diagnosis of rare diseases on a specific example. The article presents the possibilities of virtual diagnosis of a clinical case — a child with congenital hypothyroidism complicated by fever of unclear genesis. The authors presented a web application that allows reproducing the process of differential diagnosis in order to clarify the genesis of prolonged subfebrile fever. At each stage of virtual diagnosis, a user is supposed to analyze all the information about the patient and make a decision: plan further examination, «refer» the patient to specialists for consultations, while forming diagnostic hypotheses. As a result of passing the case, the integral score — the sum of points for correct answers — is calculated and displayed on the screen. Repeated performing of virtual diagnosis usually increases the score, and, most importantly, helps to consolidate the knowledge necessary for correct diagnosis. Interactive clinical case can be used in the training process of clinical residents, medical students as an additional tool. It can also be applied for pediatricians’ professional upgrade for they can be exposed to this pathology. Application of case method in education allows to guide the learning physician through the stages of virtual diagnosis, to evaluate the accuracy of his decisions and to explain the mistakes made while solving the case.