OBJECTIVE: To evaluate the effect of a new formula of a chlorhexidine-thymol varnish on mutans streptococci (MS) colonization and fissure caries development. METHODS: The study group consisted of 58 healthy adolescents (12-17 years old) undergoing orthodontic treatment with fixed appliances. A double-blind split-mouth design was applied, and 116 pairs of molar teeth were randomly assigned to topical varnish applications with either the new Cervitec Plus or its predecessor Cervitec. Both varnishes contained 1% CHX and 1% thymol (CHX/T) as active ingredients, but differed with respect to adhesive properties. The varnishes were applied in the fissures at baseline, and then every sixth week throughout the 48-week study period. Endpoints were MS colonization (CRT test) and occlusal laser fluorescence (LF, DIAGNOdent) recordings carried out regularly during follow-up. RESULTS: A significant reduction in the levels of MS in the fissures after the initial treatment was displayed with both varnishes (p < 0.05), and the levels remained consistently suppressed throughout the follow-up period. A non-significant but clear tendency was noted in favor of the new formula after six and 12 weeks, with fewer teeth harboring high counts (> or = 10(5) CFU) of MS (6w:12% vs. 24%, 12w:16% vs. 26%). No new lesions were registered in any subject, and the mean LF recordings did not change significantly over time in the groups. CONCLUSION: There were no statistically significant differences between the CHX/T varnishes in terms of bacterial growth and caries prevention. For MS suppression, a tendency towards an initially superior effect was displayed with the new formula.