Background: Streptococcus mutans play an important role in occurrence of dental caries objective: to compare the clinical and microbiological antibacterial outcomes of Mineral trioxide aggregate (MTA) and Calcium hydroxide cement Ca(OH)2. Methodology: 20 primary molars in 10 children with year's 5-9 y .For each child one tooth was treated with Ca(OH)2 and the other with MTA. Finally, all the cavities were restored using compomer restorative material, and then microbiological parameters were recorded. Results: MTA treated teeth did not show any clinical sign or symptoms of failure. While three teeth treated with Ca(OH)2 were excluded because of necrosis. Changes in color and consistency of dentin were nearly the same for both groups. Microbiological evaluation showed a decrease in the count of Str. mutans with calcium hydroxide and complete killing of bacteria with MTA. Conclusion: The treatment showed satisfactory results of MTA as it was more potent inhibitor of bacterial-growth than Ca(OH)2.