Summary. Recurrent aphthous stomatitis is one of the most common diseases of the oral mucosa. One of the most substantiated theories of the occurrence of ASD is the role of immunobacterial mechanisms. The purpose of this study was to study the composition of the microbiota of the oral mucosa and recurrent aphthae in children. Materials and methods. To solve these problems, 35 children with aphthous stomatitis aged 7 to 14 years were examined. The patients underwent a microbiological study of the microbiota from the lesion (aphtha) and the unaffected oral mucosa. Results and discussion. 15 types of microorganisms, represented by aerobes and anaerobes, were identified. Streptococcus significantly enriches the microbiota of the oral mucosa, and Streptococcus and E. Coli, S. epidermidis significantly enrich the microbiota of the aphthae. In addition, the number of yeast-like cells of the genus Candida in the lesions significantly increases (7.13±2.68 lg CFU/ml). In children from the surface of the aphthae there was an increase in the number of S. mutans, 5.47±1.83 lg CFU/ml, than in the SB, where the number was 2.35±0.12 lg CFU/ml, with an incidence of 93% and 100%, respectively. S. sanguis was found equally in both groups (100%), the amount of infestation of which did not differ significantly. S. aureus and Klebsiella spp. were found in 93% and 18% of cases, respectively, only in aphthae, and the number was significantly high (p 0.001) 5.13±1.68 lg CFU/ml and 4.13±1.38 lg CFU/ml, respectively, than on CO Conclusion. A change in the microflora in the oral cavity was established in all children with recurrent aphthous stomatitis - a decrease in the lesions (aphthae) in the content of representatives of Streptococcus in bacterial communities, Lactobacillus with an increase in the number of yeast-like cells of the genus Candida and the appearance in the biocenosis from the surface of aphthous ulcers S. aureus, E. coli and S. epidermidis; Streptococcus significantly prevails on the oral mucosa, and Streptococcus and E. coli, S. Epidermidis reliably colonize aphthae.