Aims: Our purpose was to systematically review the literature on the effectiveness of chlorhexidine varnish for preventing dental caries in children and adolescents and to determine its effectiveness compared to fluoride varnish. Methods: MEDLINE, EMBASE and the Cochrane Library were searched through December 2009 to identify relevant randomised trials with blind outcome assessment and a minimum duration of 1 year. The search was later updated in MEDLINE and the Cochrane Library to March 19th, 2010. Risk of bias of the included trials was assessed. The primary outcome was the caries increment. Results: Twelve trials met the inclusion criteria for the review. There was considerable variation between trials in the concentration and frequency of application of the chlorhexidine varnish, in baseline caries levels and in background exposure to fluoride. Six parallel-group trials reported no statistically significant difference in caries increment in permanent teeth with the application of chlorhexidine varnish compared to placebo or no treatment. The results of 4 split-mouth trials were conflicting: 2 trials found no significant difference in caries increment and 2 reported statistically significant results in favour of chlorhexidine varnish. One trial of the effect of chlorhexidine varnish in primary teeth demonstrated a statistically significant reduction in caries increment. The results of 1 trial comparing chlorhexidine varnish with fluoride varnish for preventing caries in adolescents were equivocal. Conclusion: Evidence regarding the effectiveness of chlorhexidine varnish for preventing caries is inconclusive. Further well-conducted randomised trials are required before chlorhexidine varnish can be recommended for caries prevention. Copyright © 2010 S. Karger AG.