Chronic recurrent oral aphthae in residents living in an ecologically unfavourable region are characterized by a permanent course and prolonged recovery processes of regeneration of pathological elements of the oral mucosa. Using the microbiological method and modern test systems, it has been found that on the surface of aphthae an extremely diverse state of the oral microbiota is determined and its types are diverse. Trigger mechanisms have been determined. The role of representatives of various types of microorganisms-entero-cocci, staphylococci, streptococci, yeast-like fungi of the genus Candida (C. albicans) and obligate-anaerobes in the development of recurrent oral aphthae has been established. The data obtained can serve as an indication for the development of modern treatment and preventive measures regarding this category of patients. © 2019, Ediciones Medicas del Sur S.R.L. All rights reserved.