The purpose of the study: to evaluate the effect of different types of direct current transcanal effects on the root canal microbiota. The study involved 91 volunteers aged 18 to 65 years, in 48 (53%) no periapical lesions were detected, in 43 (47%) periapical lesions. For determination of the optimal parameters of dosage an apex-phoresis, that provides antibacterial effect, clinical strains the facultative anaerobic of bacteria was used, after collection from root canal of teeth. The most pronounced antimicrobial action in which an electrode placed in the cavity of the tooth is connected to the plus of a current source — are transcanal anodalgvanization and apex-phoresis. For transcanal anodalvanization, these are copper ions, and for apex-foreses, a combination of silver ions and copper ions. Both methods showed high antibacterial activity against all representatives of anaerobic microbiota. The obtained data are confirmed with a molecular and genetic method of identification of the hardly cultivated virulent anaerobic bacteria using the diagnostic kit for PCR «Multident-5».