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The creation of a registry of patients with rare diseases is a priority of the National Strategy for Rare Diseases as well as of the National Plan for Rare Diseases. Knowledge of the real number of patients with rare diseases would thus, in addition to basic clinical information, represent an important point in planning health and social care. The presented work introduces points of departure which constitute the basis of a new specific National Registry of Patients with Rare Diseases in the Slovak Republic. Its creation builds on the existing registries as well as on the structure of health care in the Slovak Republic. With the protection of personal data in mind, the collection of data will be carried out by the National Centre of Health Information (NCHI), which will also use the existing tool in the process of creation. Thanks to the cooperation between NCHI and the Slovak Society of Medical Genetics, NCHI developed separate reporting forms on rare diseases according to OMIM (Online Mendelian Inheritance in Man) and ORPHANET rare disease coding (ORPHA codes of rare diseases), and the International classification of diseases code (ICD 10). The activities also include cooperation with the existing registries (part of which are rare diseases). For example National Registry of Congenital Developmental Heart Defects, national register of neuromuscular disorders, oncologic register or register of diabetes mellitus. Gathering the information from these registries we will extend the data about rare diseases in the Slovak republic. At the international level the participation in the European Surveillance of Congenital Anomalies (EUROCAT) is important.