The aim of the present study was to evaluate and compare the effects of three different chlorhexidine (CHX)-containing preparations on mutans streptococci (MS) levels in interdental plaque and whole saliva. Ninety-three healthy schoolchildren (8–10 years old) with high scores of salivary MS were selected by a screening procedure and randomised into three equally sized groups. MS were enumerated at all mesial interdental sites of the first permanent molars with aid of a modified chairside technique. The patients were then treated three times within 2 weeks with either a 1% CHX/thymol-containing varnish (group A) or a 1% CHX gel (group B), or they were subjected to daily supervised toothbrushing with a 0.4% CHX dentifrice for 1 month (group C). Follow-up samples of saliva and plaque from the interdental sites were collected 1 and 3 months after termination of treatment. A statistically significant reduction of MS levels in saliva and interdental plaque was found in all groups after 1 month. The CHX-containing dentifrice (group C) was the most effective method in reducing MS levels in saliva, and a significantly stronger (p < 0.05) suppression was found after 1 and 3 months when compared with the gel and the varnish forms. The gel (group B) tended to be slightly more effective than the varnish (group A). In the interdental plaque, the reduction of MS was less marked than in the saliva, and the three groups exhibited MS reductions of similar magnitude (20%) and duration, persisting up to 3 months. However, a high proportion (approximately 50%) of all interdental sites were relatively unaffected by the treatments. In conclusion, our results suggest that the interdental MS colonisation was difficult to combat, irrespective of CHX preparation and method, while the salivary levels were more easily affected. Daily tooth-brushing with a CHX-containing dentifrice was more effective in reducing MS in saliva compared with the gel or varnish applications.

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