According to the WHO, in the last two decades, the incidence of atopic dermatitis in children in the developed world reached 30%, which, of course, is a serious problem that requires a comprehensive investigation of the pathogenetic aspects of the disease. The effect of superantigen toxins of Staphylococcus aureus is one of the non-specific factors causing severe clinical course and exacerbations of atopic dermatitis. Objective — the objective of the study is to investigate the properties of the superantigen toxins of S. aureus in patients with atopic dermatitis for the purpose of further development of a complex therapy. Material and methods. We followed-up 32 children (17 males and 15 females) with moderate and severe atopic dermatitis. We collected 96 biological material samples from three ecotypes: from the wound surface, nasal cavity, and pharynx. The obtained material was sent for bacteriological and molecular genetic testing. Results and conclusions. S. Aureus dominated on the wound surface and in the nasal cavity (according to the results of cultural method). Toxin genes having superantigen activity were identified.