The prevention of dental caries in preschool children is a priority for dental services. The aim of the study was to investigate the caries-preventive effect of 2 fluoride varnishes in caries-active preschool children, and then compare the outcome with a non-varnish control group. After screening, 180 preschool children aged 36-71 months, with at least 1 noncavitated lesion, were enrolled and randomly allocated into 3 parallel groups, namely A: 1.5% ammonium fluoride varnish (Fluor Protector S), B: 5% NaF varnish (Duraphat), and C: professional tooth-cleaning. All children were recalled every third month for intervention and their parents were instructed to have them brush their teeth with a 1,000-ppm fluoride toothpaste twice daily. Caries were recorded at baseline and after 12 months by a calibrated examiner and the incidence was scored on noncavitated (d2) and cavitated (d3) level. We tested differences between the groups with the χ² and two-sided t tests. One hundred and seventy-two children (95.6%) completed the trial and 56 (32.6%) and 35 (19.2%) developed new d2 and d3 lesions, respectively. Both varnishes reduced the incidence of caries compared with the control group, but there was no significant difference between group A and group B. Compared with group C, the relative risk for developing cavitated lesions was 0.39 (95% CI 0.22-0.62) in group A and 0.26 (95% CI 0.14-0.50) in group B. The total prevented fraction (Δd2d3mft) for group A and group B was 19.9 and 22.5% (p < 0.05), respectively. No adverse effects were observed or reported during the study period. In conclusion, the 2 fluoride varnishes demonstrated an equal capacity to reduce the incidence of caries in caries-active preschool children over a 12-month period in comparison with a control group.