Aims:The aim of the present study was to evaluate the effect of a probiotic drop containing Lactobacillus rhamnosus, Bifidobacterium infantis, and Lactobacillus reuteri on salivary counts of Streptococcus mutans (SM) and Lactobacillus (LB) in children 3–6 years of age.Settings and Design:Sixty-one healthy children were randomly allocated into two parallel blocks in this double-blind, randomized controlled trial (IRCT2014120320202N1) from May to June 2015.Subjects and Methods:Finally 53 participants consumed five drops of placebo (n = 23) or probiotic (n = 30) every night for 2 weeks. Before intervention and 1 day after completion of the intervention, unstimulated salivary samples were collected, and microbiologic evaluations were carried out.Statistical Analysis:Data were analyzed with descriptive statistical methods Wilcoxon signed ranks, Mann–Whitney, and logistic regression.Results:SM level decreased significantly in probiotic group after intervention (P = 0.045), and there were significant differences in salivary SM counts after intervention between two groups (P = 0.04). In probiotic group, LB counts decreased significantly after intervention (P = 0.048); however, there were no significant differences between two groups (P = 0.216).Conclusions:Use of this probiotic drop decreased salivary counts of SM; however, LB counts did not change. In addition, use of the drop in children with higher salivary counts appeared to be more effective.