The purpose of this work is to demonstrate the possibility of applying the case method for teaching the diagnosis of orphan diseases on a specific example. The article presents the possibilities of virtual diagnostics of a rare clinical case — a combination of two hereditary diseases: Angelman and Wiedemann—Steiner syndromes. The authors have developed a web application that allows you to reproduce the process of differential diagnostics using multimedia technologies. At each stage of virtual diagnostics, it is necessary to analyze the information received so far about the patient, determine the plan for further examination, refer the patient for consultations to specialists and form diagnostic hypotheses. To assess the correctness of the choice of the doctor’s actions, questions are provided. As a result of passing the case, an integral score is calculated and displayed on the screen — the sum of points for correct answers. Repeated passage of virtual diagnostics usually increases the quantitative criterion, and most importantly helps to consolidate the knowledge necessary for proper diagnosis. An interactive clinical case can be used in the process of training students at medical universities as an additional tool, as well as to improve the skills of pediatricians who can meet with this pathology in their practice. The use of the case-based learning in the educational process allows not only to conduct the learning doctor through the stages of the virtual diagnostic process but also to assess the correctness of the choice of the option of their actions, to explain the wrong decision in a particular situation.