BACKGROUND The majority of the detected increment in dental caries is confined to pit and fissure surfaces of first molars. Application of pit and fissure sealants and topical fluorides are widely used procedures in the prevention of decay, and their effectiveness in caries prevention has been proved by systematic reviews. OBJECTIVE The objective of this study was to compare the effectiveness of pit and fissure sealants with fluoride varnishes in the prevention of dental decay on occlusal surfaces. METHODS Electronic searching was performed on the following databases: the Cochrane Oral Health Group's Trials Register (last update November 2005), the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2005, Issue 4), MEDLINE (from 1966 to December 2005), EMBASE (from 1974 to November 2004), SIGLE (from 1976 to December 2004), SCISEARCH, CAplus, INSPEC, JICST-EPLUS, NTIS, PASCAL (last update December 2004), DARE, NHS EED and HTA (last update November 2005). Reference lists from articles that fulfilled the inclusion criteria in this review and from review articles based on the search of MEDLINE were searched for additional relevant articles. Conference abstracts published as books or journals and handsearched by the Cochrane Oral Health Group were also included. METHODS The inclusion criteria for study selection were: random or quasi-random allocation study design; sealants versus fluoride varnish or sealants and fluoride varnish combination versus fluoride varnish alone; included studies included caries documentation on occlusal surfaces of permanent molars and the subjects were under 20 years of age. Both parallel and split-mouth study designs were accepted. The primary outcome of interest was the increment in the numbers of carious occlusal surfaces of premolars and molars. A study was excluded if sealants and fluoride varnish were not compared with each other. METHODS Two review authors carried out the baseline searches, selecting the papers on the basis of the title, keywords and abstract and making decisions about the eligibility and data extractions. The same review authors assessed the methodological quality of all included studies: for example, the allocation concealment, blinding, and completeness of follow up. Authors of the studies were contacted for additional information. Risk ratios (RR) as effect estimates were calculated for the differences in whether surfaces were carious or not in the treatment groups, along with the appropriate standard errors and 95% confidence intervals (CI). No data could be combined or meta-analyses undertaken due to the clinical and methodological diversity between study designs. RESULTS Four studies were eligible for inclusion in the review. Three of the four studies compared the effectiveness of sealants with fluoride varnish application, and one study compared the effectiveness of sealants and fluoride varnish combination with fluoride varnish alone. Results of two studies revealed the effectiveness of pit and fissure sealants to be statistically significantly higher than an application of fluoride varnish every 6 months in preventing occlusal decays of first molars at 23 months (RR 0.74, 95% CI 0.58 to 0.95) and at 9 years follow up (RR 0.48, 95% CI 0.29 to 0.79). One of these studies was classed as at low risk of bias, one of moderate to high risk. One small study at moderate to high risk of bias failed to find a statistically significant difference between sealants and fluoride varnishes. One study of low risk of bias found a statistically significant difference in favour of the sealants and fluoride varnish combination compared with merely fluoride varnish at 24 months follow up with RR 0.36 (95% CI 0.21 to 0.61). The age of children in the included studies was 5 to 9 years. Allocation concealment was classified adequate in two of these four studies. CONCLUSIONS There was some evidence of the superiority of pit and fissure sealants over fluoride varnish application in the prevention of occlusal decays. However, it remained unclear to what extent there is difference between the effectiveness of pit and fissure sealants and fluoride varnishes. Therefore, more high quality research is needed. No recommendations for the clinical practice could be given and the benefit of pit and fissure sealants and fluoride varnishes should be considered locally and individually.