Purpose: To evaluate the antibacterial characters of Glass Ionomer modified with CH on Streptococcus Mutans in Comparison With the original glass ionomer. Materials and methods: caries removal of 30 extracted primary molars, these teeth divided into three groups the first group restored with chitosan modified glass ionomer and second one restored with conventional glass ionomer and the third group restored with glacial acetic acid modified glass ionomer then sterilized at oven 60c for 72 hours. Each group was placed in mitis salivarius media with well-defined number of bacteria of streptococcus mutans, then left them for 48 hours , after 48 hours solution of each group was taken and was placed in mitis salivarius plate for another 48 hours and then bacterial counting was made to see if number of bacteria increased or decreased. Results: The Chitosan modified glass ionomer had higher antimicrobial effect than conventional glass ionomer and glass ionomer modified with glacial. Statistical analysis between the groups revealed that actually a statistically considerable difference between the all groups (P-value < 0.0001). Conclusion: Chitosan can be used as a natural material for modification of glass ionomer to increase the antibacterial effect against streptcoccus mutans and also should be supported by in vivo studies.