Purpose: to evaluate the antibacterial effect of Nutmeg natural extract on cariogenic microflora and compare its effect with chlorhexidine (CHX) in a group of Egyptian children. Subject and methods: A total of 60 normal apparently healthy children aged between 6-12 years from both genders were involved in this study and equally divided into two groups (n=30) regarding to the type of the received mouthwash: group 1; included children who rinsed with 1% Nutmeg extract containing mouth wash (Tested group); group 2; included children who rinsed with 0.12% CHX containing mouth wash (Control group). Saliva samples were collected from each enrolled child at the baseline (before the use of mouthwash), and at 7^th day after the use of mouthwash. Mitis salivarius bacitracin and Rogosa agar media were used to determine Streptococcus mutans (S. mutans) and Lactobacilli count respectively. Results: Significant reduction in S. mutans and Lactobacilli count in the two studied groups after mouth rinsing for 7 days. However, CHX showed a significant reduction in S. mutans and Lactobacilli count when compared to Nutmeg extract. Conclusions: Nutmeg extract has a significant positive antimicrobial effect against S. mutans and Lactobacilli microorganisms but the use of CHX mouthwash has a higher antimicrobial effect when compared to Nutmeg extract.