Purpose: To compare the effect of cinnamon extract mouthwash with chlorhexidine mouthwash on Streptococcus mutans counts in saliva of some children. Materials and methods: A total of 40 children from both sex were involved in the present study. Age of Children was between 6 and 12 years in a good physical condition. Children were distributed into 2 groups (A&B), each one consists of 20 children. Group A (Experimental group): each participant was given a new bottle of specific effective amount of cinnamon extract mouthwash (150ml) to be used. Group B (Control group): each participant was given a new bottle of specific effective amount of (150 ml) chlorhexidine mouthwash (0.12 %) to be used. Unstimulated salivary samples were collected and examined. Results: The average number of S.mutans was reduced significantly in cinnamon extract group and chlorhexidine group as well. Conclusion: Cinnamon extract mouthwash was successful as an antimicrobial agent and it can be used as a natural alternative to chlorhexidine.