The aim of this study is to assess the variations in the levels of Streptococcus mutans in saliva before and after short-term daily intake of the probiotic lozenge. To estimate the prevalence of S. mutans serotypes e, f, and k and its variations in salivary levels before and after short-term daily intake of the probiotic lozenge. This double-blind randomized controlled trial was conducted among 60 children of 6-12 years old, who were given lozenge twice daily containing probiotic bacteria twice daily, one in the morning and another in the evening after brushing for 1 month. The placebo lozenge group also followed the same protocol. A pre- and post-quantitative analysis of S. mutans and serotypes e, f, and k level were done in the saliva of both experiment and control groups. The data thus collected were statistically evaluated using repeated measures of ANOVA, followed by post hoc test and independent t-test. When compared with baseline, a significant reduction of S. mutans was seen after 1 month intervention and 6 months follow-up. The prevalence of serotype e was found to be 5% and serotype k was found to be 12%, whereas none of the samples carried serotype f. Future long-term research with a larger sample size is required to determine the prevalence of S. mutans serotype and longer evaluation period is required to assess the preventive role against caries development.