Statements of problems: While there are multiple components of preventive programs developed for caries prevention in children, perhaps none is as important and effective as the appropriate use of fluoride. The primary caries preventive effects of fluoride result from its topical contact with enamel and through its antibacterial actions. Till now bulk of research exists which has compared the antibacterial effects of ordinary topical fluoride gels & solutions. Little or no evidence is seen to tell us which topical fluoride including varnishes is more antibacterial. We suggested further research about antibacterial effect of APF gel and NaF varnish against cariogenic microorganisms (streptococcus mutans & lactobacillus), so use of these may have benefit in reduction of caries.Purpose: Comparison of inhibitory effect of NaF-varnish versus APF-gel on concentration of cariogenic bacteria (streptococcus mutans & lactobacillus), was the primary goal of this research.Materials and method: In this exprimental study, twenty premolars were sectioned buccolingually. With the use of "window method" certain surfaces of enamel were covered with APF-gel and NaF-varnish. Then, the number of streptococcus mutans and lactobacillus were counted after 18, 24 and 48 hours. In the "Disk diffusion" method the streptococcus mutans with the concentration of 108/ml and volume of 0.1cc were introduced to the M.S.Media culture after application of APF gel and NaF varnish. Then the inhibition zone, measured. Statistical analysis in this research was multilevel modeling.Results: The comparison between gel and varnish after 18, 24 and 48 hours showed that gel has more effect than varnish over the number of lactobacillus. The difference with lactobacillus was statistically significant (p<0.005), but with streptococcus Mutans was not. APF gel was more effective (70.23%) than NaF varnish.  Conclusion: Based on the obtained results, APF gel can be used with more thrust than NaF varnish in caries prevention.Key words: APF gel, NaF varnish, Streptococcus mutans, Lactobacillus, Antibacterial