Currently, there are more than 8000–10000 rare disease (RDs), among which 75–80% are hereditary. In the Russian Federation (RF), patients are provided medical care in accordance with two lists: 17 chronic progressive and life-threatening diseases (RLTDs) and 14 high-cost nosologies (HCNs). The study was aimed to assess the range, prevalence, and genetic epidemiological characteristics of the RDs from the lists of RLTDs and HCNs in the Republic of North Ossetia–Alania and RF in general. We determined the number of patients from the RLTD (a total of 18,744 people in the RF, among them 8713 children; 129 and 42 people, respectively, in the Republic of North Ossetia–Alania) and HCN (28727 people/13454 children in the RF; 554 and 64 in the Republic of North Ossetia–Alania) lists and calculated the prevalence per 100,000 population. The global prevalence of RDs was estimated using the Orphanet database. The average prevalence of RLTDs in the whole population of the RF was 11.51 cases and that among children was 25.08. Similar data were obtained for the Republic of North Ossetia–Alania (19.38 and 29.44, respectively). It was found that idiopathic thrombocytopenic purpura, disorder of the complement system, maple syrup urine disease, porphyria were more common in the Republic of North Ossetia–Alania than in the RF in general, while galactosemia was less common. The analysis of disorders from the RLTD list has shown lower prevalence of hemophilia and pituitary dwarfism in the Republic of North Ossetia–Alania compared to the RF and Orphanet, along with the higher prevalence of type VI mucopolysaccharidosis, hemolytic uremic syndrome, and systemic juvenile rheumatoid arthritis. In the Republic of North Ossetia–Alania, the features of the range of genetic variation in the genes РАН (phenylketonuria) and CFTR (cystic fibrosis) have been identified. Thus, assessment of the RD prevalence in the regions is important and essential for raising awareness of medical personnel, as well as for expansion and improvement of medical care provision to patients with RLTDs and HCNs.