Objective: To evaluate the effect of a new chlorhexidinefluor ide varnish on mutans streptococci (MS) counts and laser fluorescence (LF) readings in fissures of permanent molars. Method and Materials: The study group consisted of 57 healthy schoolchildren (7 to 14 yrs) that volunteered after informed consent. A double-blind split-mouth design was employed and 87 pairs of non-cavitated permanent molars were randomly assigned to treatments with either chlorhexidine- fluoride varnish (CHX-F) or chlorhexidine-thymol varnish (CHX-T, Cervitec Plus) as active control. The varnishes were topically applied at baseline and every sixth week throughout the 24-week study period. Endpoints were MS counts (CRT test) and occlusal LF readings (DIAGNOdent pen) registered regularly during follow-up. Results: At baseline, > 50% of the occlusal fissures harbored high MS counts (≥ 10⁵ CFU), but a significant decrease (P < .05) was found after treatment with both varnishes. After 24 weeks, less than 5% exhibited high counts. There were no significant differences between the varnishes at any time point. The mean LF values were similar in both treatment groups at baseline, but a significant reduction (P < .05) was scored in the CHX-F group after 12 and 24 weeks. A similar reduction was found also in the CHX-T group after 24 weeks. No adverse events were reported. Conclusion: There were no significant differences between the CHX-F and CHX-T varnishes in terms of MS suppression after four applications over 24 weeks. Both varnishes also reduced the LF readings significantly compared with baseline, but further long-term studies are needed to confirm a caries-preventive effect.