The problem of rehabilitation of children with congenital cleft lip and palate (CCLP) is a difficult task and doesn’t lose its relevance. Children with CCLP often suffer from repeated acute viral and bacterial infections of the respiratory tract and upper respiratory tract, which leads to a forced delay in surgical, orthodontic treatment, adequate speech therapy and complications after staged surgical operations. The development of inflammatory processes in children with CCLP is associated with anatomical and topographic features that facilitate the penetration of pathogenic microflora in oral and nose mucosa and, consequently, negative changes in the immune system (IS). The key cells of IS in maintaining homeostasis and ensuring oral health are neutrophil granulocytes (NG). NG dysfunctions in CCLP interfere with the elimination of pathogens and support their persistence. This can occur against the background of previously existing defects in the functioning of the NG system and is aggravated by the significant pathogenicity and massiveness of the impact of various infectious agents. Full diagnostics of NG dysfunctions is necessary for the further implementation of their timely immune correction and prevention of the development of pathological chronic inflammation in response to the pathogenic microflora long-term on the mucous membrane of the mouth and nose. For this purpose study was conducted of the functional activity and phenotypic characteristics of NG in children with CCLP at different stages of complex rehabilitation. Blood samples of 56 children with CCLP 1-3 years (n = 20, group 1), 4-6 years (n = 20, group 2), and 7-12 years (n = 20, group 3) at different stages of complex rehabilitation and 30 conditionally healthy children (control groups) of the corresponding age was studied. A violation of the microbiocenosis of the mucous membranes of the oral and nasal cavities was revealed, which may be a cause or a consequence of a decrease in antibacterial immunity, first of all NG dysfunctions. Common for all age groups children with CCLP NG dysfunction was found: the appearance of NG expressing CD14 receptors that are absent in children of all three control groups, which indicates the presence of viral and bacterial load; defects of phagocytosis associated with a decrease in the number of actively phagocytic NG, impaired NG capture functions; impaired NADPH oxidase release with partial or complete blockade of the response to additional antigenic load, even in the absence of acute clinical manifestations. Comparative analysis of the studied indicators of the expression level of the receptors CD64, CD16, CD32, CD14 NG in children with CCLP demonstrates different equipment, which determines the inconsistency of the phagocytic and microbicidal function of NG in different age periods. Thus, an increase in the expression of these membrane markers, especially CD64 and CD14, in older age groups is accompanied by more significant defects in phagocytic and killing functions of NG, which is associated not only with recurrent viral respiratory infections, but also with a high frequency of associated bacterial infections of the respiratory system and ENT – organs. Revealed NG dysfunctions in children with CCLP of various age groups indicate their inability to implement adequate anti-infective protection, which can lead to atypically occurring viral – bacterial infections and the occurrence of various, including purulent complications in the postoperative period, which requires the development of targeted immunotherapy, included in the program of comprehensive rehabilitation in children with CCLP and aimed at restoring impaired NG functions.