Purpose: This study was conducted to evaluate the effect of Thyme extract mouth rinse against Chlorhexidine mouthwash on salivary Streptococcus mutans count in a group of Egyptian children. Materials and Methods: A total of 70 Egyptian children were included in this study. Children ages ranged from 5 to 10 years old in a good physical condition. Children were randomly distributed into two groups A & B each of 35 children. In children of group A (using Thyme extract) each participant was instructed to rinse with 10ml of thyme extract for one minute. In group B (control group using Chlorhexidine mouthwash 0.2%) each participant was instructed to rinse with 10ml of CHX for one minute. Results: There was a significant reduction in Streptococcus mutans count in both groups. Conclusion: Thyme extract mouthwash was successful as an antimicrobial agent. It significantly reduced the total bacterial count in the saliva of children when compared to a potent antiseptic like Chlorhexidine.