Background: An anti-cariogenic diet containing probiotics can be effective in caries prevention. This animal study compared the effects of milk and yogurt on Streptococcus sobrinus counts and caries score. Materials and Methods: A total of 36 male rats were infected with S. sobrinus (27,607) and divided into three groups. Group A and B received 200 mL of milk and 100 g of yogurt per day, respectively, and a control group received 2.5 mL of NCP number 2 diet twice daily for 21 days. After killing the animals, their lower left jaws were removed and sonicated to quantify the colonies of S. sobrinus. Dental caries was scored using Keyes technique. Data were analyzed using ANOVA and Kruskal-Wallis, Mann-Whitney and Wilcoxon-Signed Rank tests. Statistical significance was set at P < 0.05. Results: The mean (±standard error of the mean) of S. sobrinus colonies in the milk, yogurt and control groups were determined at 119666.67 (±20733), 46416.666 (±12846) and 163,250 (±33493), respectively. Microbial counts decreased in the yogurt group compared with the milk and control groups (P = 0.004 and P = 0.000; respectively). There were significant differences between caries scores of smooth surfaces in the milk and yogurt groups compared with the control group (P = 0.000 and P = 0.000, respectively). Both milk and yogurt significantly reduced caries score of fissured surfaces compared with controls (P = 0.004 and P = 0.000, respectively). Conclusion: Considering the limitations of this study, yogurt administration reduces S. sobrinus counts. In addition, yogurt and milk regimens reduce the caries scores of smooth and fissured surfaces.