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Chromosomal diseases are, although rare, a pressing problem for pediatric practice. Rare forms of diseases are considered to be those diseases whose prevalence in the population is less than 10 cases per 100,000 people. Such nosologies include Orbeli syndrome, a severe orphan disease described in 1962 by N. Wang. The rarity of the disease causes isolated cases of description of this syndrome in the literature. However, there are known examples of Orbeli syndrome in newborns, infants, children aged 6 and 13 years, and even in adults. Clinically, this syndrome most often manifests itself as gross malformations of organs and systems, delayed physical and neuropsychic development. The case of Orbeli syndrome presented in the article was confirmed by karyotyping (46, XY, del(13)(q22)). Clinically, the disease was characterized by multiple congenital malformations in the form of microcephaly, hypospadias, cryptorchidism, deformation of the ankle joint, contracture of the knee joints, varus position of the feet, cleft of the hard and soft palate. Instrumental examination revealed alobar holoprosencephaly, renal hypoplasia and congenital heart disease. The results of expanded neonatal screening made it possible to diagnose the child with primary immunodeficiency and a disorder of amino acid metabolism. The child was recognized as in need of palliative medical care. An unfavorable prognosis for life based on the totality of the pathology has been established. This clinical case highlights the importance of widespread implementation of whole exome sequencing of future parents when planning pregnancy in order to prevent such severe nosologies.