The purpose of this study was to determine the efficacy of fluoride varnish (FV) in inhibiting progression of secondary caries (SC). In a first experiment, human teeth, restored either with amalgam or resin composite, were exposed for 4 days to a microbial caries model. Half of each specimen was then painted with an acid-resistant nail varnish to maintain the baseline SC lesion. Specimens were then either treated with a FV (removed after 24 h) or not treated (control groups) prior to being exposed for 4 more days to the caries model. A second experiment was conducted to compare the effect that the varnish (with and without fluoride) had on SC development around amalgam. Confocal laser scanning microscopy data from these experiments suggested that the application of a FV to early, active SC lesions significantly slowed down their progression. Furthermore, the application of a placebo varnish showed a trend towards slowing down lesion progression, suggesting that the effect of FV on SC is not only due to its fluoride release.