Background: A growing number of dentists are embracing the philosophy that natural agents are better for children's oral health. Knowledge of probiotics on host immune system has entered a new phase of research, and progression in this field is likely to offer novel means by modulating host immunity for prevention and treatment of a wide variety of oral diseases. Aim: To compare the antimicrobial efficacy of probiotics in reducing salivary Candida albicans counts with commonly used antimicrobial agents like 0.2% chlorhexidine and herbal rinse. Materials and methods: A randomized clinical trial was conducted on 60 subjects aged between 6 and 14 years, for a period of 9 months. The subjects were randomly divided into three groups comprising 20 subjects in each group. Three oral agents were administered twice daily for a maximum period of 1 week. Candida albicans counts were recorded before and after intervention and the results were submitted for statistical analysis using Statistical Package for the Social Sciences (SPSS) version 15.0 software. Results: The change in mean log₁₀ colony-forming unit (CFU)/ml of C. albicans in groups A to C was 0.43 ± 0.72, 0.68 ± 1.05 and 0.22 ± 0.66 CFU/ml respectively. Conclusion: Data obtained from the study demonstrated that probiotic rinse was equally effective as 0.2% chlorhexidine digluconate rinse in reducing C. albicans counts after 1 week of intervention. Herbal oral rinse was least effective. Probiotic oral rinses have opened new horizons in improvement of oral health by maintaining healthy ecosystem. However, a longitudinal study with larger sample size needs to be undertaken to evaluate the therapeutic effects of probiotics and herbal agents. How to cite this article: Mishra R, Tandon S, Rathore M, Banerjee M. Antimicrobial Efficacy of Probiotic and Herbal Oral Rinses against Candida albicans in Children: A Randomized Clinical Trial. Int J Clin Pediatr Dent 2016;9(1):25-30.