The article presents the results of analysis of spectrum, the rate of frequency and the amount of microorganisms in oral liquid before the beginning of orthodontic treatment of dental abnormalities and deformations and in its stages (6 and 12 months later). As the result of the study the appearance of pathologic microorganisms Staphylococcus aureus and a great number of conditionally-pathogenic fungi of Candida family and Porphyromonas spp. were determined. The obtained results show the need of elaboration of standards for the treatment of orthodontic patients.