A lack of the single criterion for classifying rare diseases as a group of orphan diseases is the main current problem. First, it is associated with rare detection of symptoms among patients, especially children. Second, specialists have a limited number of methods of detecting orphan diseases. As the disease is considered rare, it is not profitable for pharmaceutical companies to produce the preparations which are purchased not in large numbers, but in single packages, because expenses on clinical trials and marketing advertising exceed return of investment. The market of orphan drugs in Russia is at the stage of development and formation. Medical organizations that carry out medicinal therapy of patients with orphan diseases require a clear set of regulatory documents ensuring provision of medical and pharmaceutical aid. Special attention should be paid to drawing up the lists of medicinal preparations to treat the patients. Personified accounting of patients with detected orphan diseases is an important stage for medical and pharmaceutical organizations. Modern diagnostics of orphan diseases at early stages, especially in children, exploration of specialized genetic methods of research and making them accessible for the population constitute an essential problem.