The problem of antiseptic processing root canal during endodontics for the treatment of periodontal disease is dealt with in the article. Perfusion activity of various antiseptics ( hypochloran , chlorhexidine, dimephosphon ) is studied, their comparative analysis is performed. According to the result dentin is the most permeable to dimephosphon and hypochlorana , the least - for chlorhexidine. The author remarks the unevenness of dentin permeability in the mesial distal and vestibular oral direction.