The article provides an overview of special literature, which gives an opportunity to redefine some issues of disability prevention in children with rare (orphan) diseases, which will improve the organizational measures in this area. The prevention of children’s disability is considered as a system of measures to protect the health of the mother and child throughout childhood. The early disability prevention system in children and support for families raising children with disabilities remain among the main priorities of the State social policy of the Russian Federation. The authors describe modern technologies for reducing the genetic burden in the population from the point of view of preventing hereditary and congenital pathologies. They identify the priority areas of disability prevention in children with rare (orphan) diseases, i.e. introduction of prenatal and preimplantation diagnostics; use of the Prenatal Consultation organizational model; conducting a wider screening for congenital and hereditary metabolic diseases with the inclusion of the most common nosological forms of rare (orphan) diseases; finding pathogenetic therapy methods; increasing the knowledge of pediatricians about rare (orphan) diseases.