The aim of the study was to compare the efficacy of a 40% chlorhexidine (CHX) varnish (EC40, Certichem, Nijmegen, The Netherlands) with a 1% CHX-0.2% NaF gel in decreasing the level of salivary mutans streptococci (MS). The subjects were screened for a high level of MS using a Dentocult-SM® strip method (Orion Diagnostica, Finland). In varnish groups with fluoride (VCHXF, n = 20) and without fluoride (VCHX, n = 19), the CHX varnish was applied on dry teeth using an ampoule and an anesthetic syringe with blunt needle, and removed after 15 min. In group VCHXF an additional 2.26% fluoride varnish (Duraphat®, Woelm Pharma GmbH, Eschwege, Germany) was applied. The CHX-NaF gel treatment included the application of the gel with rubber cups and dental tape for 5 min on three occasions during a week in group GCHXF (n = 21). The level of MS (MSB agar) was significantly lower after 4 weeks than at baseline in VCHX (p CHXF (p CHXF a significant decrease (p = 0.001) was observed after 4 weeks only with the strip method. In VCHX and VCHXF the strip values for MS were still reduced after 12 weeks. In VCHX and GCHXF a small, although statistically significant, increase was observed in the total number of microorganisms after 4 and 12 weeks. Opinions on taste sensations associated with the treatments were generally negative, but least negative in the VCHXF group; fewer side effects were also reported in the VCHXF group. The results indicate that one treatment with CHX varnish gives an equal or a longer suppression of salivary MS than three treatments with the gel form. Although the concentration of CHX is high, the varnish was associated with fewer side effects and complaints of bad taste than the 1% CHX-NaF gel, especially when coated by a fluoride varnish. This is probably due to an accurate application on teeth with a minimal contact with the oral mucosa.