In recent years, in the Russian Federation, the program of state guarantees of free medical care to citizens has included expanded neonatal screening, including for rare diseases. At the same time, it is important to understand the economic impact of this initiative on the state budget. On the one hand, timely detection of diseases allows for better control in their treatment. On the other hand, this will require more healthcare resources and, as a result, additional budgetary expenses. The purpose of the study is to develop an algorithm for calculating the economic impact of introducing neonatal screening for rare diseases. The regulatory documents regulating the provision of medical care, as well as neonatal screening for rare diseases, were analyzed. As an example for the development of the algorithm, a study was used to assess the socio-economic effectiveness of neonatal screening for spinal muscular atrophy in the Russian Federation, as well as examples of domestic pharmacoeconomic studies. The main types of costs that need to be assessed in the economic analysis of the consequences of introducing screening are identified. Approaches to their accounting are presented based on existing regulatory documents.