Background: Nanoparticles are clusters of atoms in a size range from (1-100) nm. Nano dentistry creates amazing useful structures from individual atoms or molecules (nanoparticles), which provides a new alternative and a possibly superior strategy in prevention and treatment of dental caries through management of dental plaque biofilms. The aim of the study was to test the sensitivity of Streptococcus mutans to different concentrations of hydroxyapatite and iron oxide nanoparticles suspension solutions, in comparison to chlorhexidine, and de-ionized water, in vitro. Materials and methods: Agar well technique was applied to test the sensitivity of Streptococcus mutans to different concentrations of hydroxyapatite and iron oxide nanoparticles compared with chlorhexidine 0.2% as a control positive and de-ionized water as control negative. Zone of inhibitions which is clear zone of no growth of the bacteria were measured across the diameter of each well, no zone indicated a complete resistance of bacteria to the agents. Results: Values of mean of inhibition zone for all concentrations of hydroxyapatite nanoparticles were zero. While for iron oxide nanoparticles, they were zero until reaching the last three concentrations, in which there was a respective increase with a highly significant difference between groups (p>0.01). When making multiple comparisons of the inhibition zones of iron oxide nanoparticles between groups, findings showed that the inhibition zones of 17%, 20% and 22.5% of iron oxide nanoparticles were more than all other concentrations that had no inhibition zones with a significant difference (p>0.05). There was a highly significant difference between each concentration of hydroxyapatite and iron oxide nanoparticles with chlorhexidine and de-ionized water (p>0.01). Conclusion: Streptococcus mutans were not sensitive to hydroxyapatite nanoparticles, as there was a complete resistance for the agent. While for iron oxide nanoparticles, Streptococcus mutans were sensitive to 17.5%, 20% and 22.5% and sensitivity increased with the increase in concentration with a statistically highly significant difference and this indicates an antibacterial activity of this material. Keywords: Hydroxyapatite nanoparticles, Iron oxide nanoparticles, streptococcus mutans, Inhibition zone. (J Bagh Coll Dentistry 2018; 30(1): 69-75)