Purpose: This study was conducted to evaluate the effect of two mouth rinses (pomegranate fresh juice and pomegranate peel extract), against chlorhexidine mouthwash on salivary S.mutans count in a group of Egyptian children. Material and Methods: A total of 45 Egyptian children from both sex were included in this study. Children age ranging from 5 to 10 years old in a good physical condition. Children randomly were distributed into three Groups A, B & C, each of 15 children in each group. Group A (using pomegranate fresh juice): consisted of fifteen children, each participant was instructed to rinse with 35ml of pomegranate fresh juice wash about 2 minutes. Group B (using pomegranate peel extract): consisted of fifteen children, each participant was instructed to rinse with 35ml of pomegranate peel extract wash about 2 minutes. Group C (Control group chlorhexidine mouthwash 0.2%): consisted of fifteen children, each participant was instructed to rinse with 35ml of chlorhexidine mouthwash wash about 2 minutes. Results: There was a significant reduction in mean Streptococcus mutans count in the 3 groups after the study. Conclusions: Pomegranate (peel & juice) mouthwash was successful as an antimicrobial agents. It significantly reduced the total bacterial count in the saliva of children when compared by a potent antiseptic like 0.2% chlorhexidine.