Hypertrophy of pharyngeal lymphoid tissue is among the most common problems in pediatric otorhinolaryngology, in particular, hypertrophy of the palatine tonsils. This disorder is characterized by increased size of a single or both palatine tonsils combined with various clinical symptoms. The principles of treatment in children with this pathology remain debatable, since the long-term effects of bilateral tonsillotomy are still not fully understood. The aim of the study was to assess the expression levels of genes encoding the innate immunity molecules (TLR4, HBD1, HBD2, IL1β) in the mucous membranes of palatine tonsils in children with palatine tonsillitis before and after treatment.We conducted a study of 78 patients divided into three independent groups. The 1st group (comparison) included 20 somatically healthy children. The 2nd group included 28 children with grade 2 palatine tonsil hypertrophy who underwent local treatment. The 3rd group included 30 children with grade 3 hypertrophy of the palatine tonsils, who, by clinical indications, underwent bilateral tonsillotomy. Determination and evaluation of innate immunity indices was carried out both before starting the treatment, and one month later, using the real-time PCR method.In children with hypertrophy of palatine tonsils, the initial values of TLR4 gene expression and antimicrobial peptides differed from those of healthy children. A decreased expression of HBD1 and HBD2 genes, which provide immediate protection against pathogens, was revealed. The values of TLR4 gene expression differed in groups of children with varying degrees of palatine tonsillar hypertrophy. In patients with bilateral tonsillotomy, an increased expression of TLR4 gene and a decreased expression of antimicrobial peptide genes (HBD1, HBD2) were revealed, which may indicate a readiness for development of tonsillar inflammation in response to pathogens. One month after surgical treatment, the indices of innate immunity were comparable with those of healthy children thus confirming the validity of surgical treatment. In the 2nd group of patients, the TLR4 gene expression one month after conservative treatment remained reduced, the expression of β-defensin HBD1 gene increased and exceeded the indicators of the group of healthy children, the expression level of the IL-1β gene was reduced.The revealed imbalance between the TLR4, HBD1 and HBD2 expression levels confirms an important role of innate immunity mechanisms in pathogenesis of palatine tonsillitis. The assessment of innate immunity indices may be used as an additional criterion in administration of therapy for hypertrophy of palatine tonsils and evaluation of its efficiency.