In the prevention of root surface caries, antimicrobial therapy for the control of subgingival and supragingival plaque is seriously considered as a long term suppression of pathogenic microflora. Recently, varnishes containing antimicrobial agents have been developed to control the supragingival microflora. The purpose of this study was to determine the antimicrobial effects of 20% chlorhexidine varnish and 2.6% silane fluoride varnish with sealant. In clinical experiments, 12 subjects were selected from the periodontally treated patient and divided into 3 groups. After a dental prophylaxis, the subjects were treated with single application of placebo varnish (group I), 20% chlorhexidine varnish (group II), and 2.6% silane fluoride varnish (group III). Root surface plaque samples were taken before (baseline) and one, two, four, and 8 weeks after the treatments. Microbiological examinations of root surface plaque were performed with culture study and indirect immunoflorescence (I.I.F.) study, and immunological examination of gingival crevicular fluid antibody titers was performed with ELISA study. The results were as follows: 1. Pathogenic microflora on the root surface including S. mutans, S. sanguis, S. mitis, A. naeslundii, A. viscosus were 24 - 37% on I.I.F. study. 2. S. mutans, S. sanguis, S. mitis, A. naeslundii, A. viscosus of the root surface plaque was significantly reduced from 1 week to 8 weeks after antimicrobial varnish treatment, but showed generally increasing tendency in control group. 3. Gingival crevicular fluid antibody titers were significantly reduced from 1 or 2 weeks to 4 weeks after antimicrobial varnish treatment.