Background: To ensure rare disease patients with medicines is a challenge for the health system. Treatments for rare diseases are very expensive, so the main financial burden for providing patients with medicines lies with the state. The objective of the study was to identify the aspects related to the optimization of process of assurance with medicines the patients with rare diseases. Material and methods: Retrospective study was performed using systemic analysis methods. Data were collected and processed with reference to health programs in the field of rare diseases and centralized public procurement. Results: The mechanism by which “rare” patients are provided with medicines and major problems related to was analyzed. The National Program “Combating rare diseases” represents the first stage by identifying the rare diseases that most frequently affect patients in the Republic of Moldova. Treatment options and annual medicines requirements are set in accordance with national clinical protocols and international guidelines recommendations, the number of patients on the doctor’s records, as well as statistical data. Conclusions: Major problems in ensuring medicines to patients with rare diseases have been identified. The need of medicines is ensured by centralized public procurement, from the financial resources of the state budget, which were analyzed for the period of years 2018-2020.