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 < 0.001) and VCHXF (p < 0.05), but not after 12 weeks. In GCHXF 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.(ABSTRACT TRUNCATED AT 250 WORDS)