BACKGROUND Topically-applied fluoride varnishes have been used extensively as an operator-applied caries-preventive intervention for over three decades. This review updates the first Cochrane review of fluoride varnishes for preventing dental caries in children and adolescents, which was first published in 2002. OBJECTIVE To determine the effectiveness and safety of fluoride varnishes in preventing dental caries in children and adolescents, and to examine factors potentially modifying their effect. METHODS We searched the Cochrane Oral Health Group's Trials Register (to 13 May 2013), the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2013, Issue 4), MEDLINE via OVID (1946 to 13 May 2013), EMBASE via OVID (1980 to 13 May 2013), CINAHL via EBSCO (1980 to 13 May 2013), LILACS and BBO via the BIREME Virtual Health Library (1980 to 13 May 2013), ProQuest Dissertations and Theses (1861 to 13 May 2013), and Web of Science Conference Proceedings (1945 to 13 May 2013). A search for ongoing trials was undertaken on ClinicalTrials.gov on 13 May 2013. There were no restrictions on language or date of publication in the search of the electronic databases. METHODS Randomised or quasi-randomised controlled trials with blind outcome assessment used or indicated, comparing topically-applied fluoride varnish with placebo or no treatment in children up to 16 years during at least one year. The main outcome was caries increment measured by the change in decayed, missing and filled tooth surfaces in both permanent (D(M)FS) and primary (d(e/m)fs) teeth. METHODS At least two review authors assessed all search results, extracted data and undertook risk of bias independently. Study authors were contacted for additional information. The primary measure of effect was the prevented fraction, that is the difference in mean caries increments between the treatment and control groups expressed as a percentage of the mean increment in the control group. The caries increments nearest to three years were used from each included study. Random-effects meta-analyses were performed where data could be pooled. Potential sources of heterogeneity were examined in random-effects meta-regression analyses. Adverse effects information was collected from the included trials. RESULTS Twenty-two trials with 12,455 participants randomised (9595 used in analyses) were included. For the 13 that contributed data for the permanent tooth surfaces meta-analysis, the pooled D(M)FS prevented fraction estimate comparing fluoride varnish with placebo or no treatment was 43% (95% confidence interval (CI) 30% to 57%; P < 0.0001). There was substantial heterogeneity, confirmed statistically (P < 0.0001; I(2) = 75%), however this body of evidence was assessed as of moderate quality. The pooled d(e/m)fs prevented fraction estimate was 37% (95% CI 24% to 51%; P < 0.0001) for the 10 trials that contributed data for the primary tooth surfaces meta-analysis, also with some heterogeneity (P = 0.009; I(2) = 59%). Once again this body of evidence was assessed as of moderate quality. No significant association between estimates of D(M)FS or d(e/m)fs prevented fractions and the pre-specified factors of baseline caries severity, background exposure to fluorides, application features such as prior prophylaxis, concentration of fluoride, frequency of application were found. There was also no significant association between estimates of D(M)FS or d(e/m)fs prevented fractions and the post hoc factors: whether a placebo or no treatment control was used, length of follow-up, or whether individual or cluster randomisation was used, in the meta-regression models. A funnel plot of the trials in the main meta-analyses indicated no clear relationship between prevented fraction and study precision. In both methods, power is limited when few trials are included. There was little information concerning possible adverse effects or acceptability of treatment. CONCLUSIONS The conclusions of this updated review remain the same as those when it was first published. The review suggests a substantial caries-inhibiting effect of fluoride varnish in both permanent and primary teeth, however the quality of the evidence was assessed as moderate, as it included mainly high risk of bias studies, with considerable heterogeneity.