This study was conducted to investigate the effect of different concentrations of chlorhexidine and calcium hydroxide on staphylococcus aureus bacteria isolated from the roots of the teeth of patients. As the bacteria were isolated from one of the patients arriving at the Teaching Hospital of the Faculty of Dentistry / University of Tikrit by taking a swab from the ends of the tooth root, and it was implanted and grown in media prepared for this purpose in the microbiology laboratory of the College of Veterinary Medicine / University of Tikrit. Graduated concentrations were used respectively from the chemical solutions of chlorhexidine and calcium hydroxide (0.5%, 1%, 2%, 4%).  Minimum Inhibitory (MIC) and Minimum Bactericidal Concentration (MBC) were calculated for the samples and it was found through the study that the concentration 2% of chlorhexidine compound after 36 hours caused inhibition of bacterial growth, as the tubes appeared transparent. The calcium hydroxide compound was found to cause inhibition of bacterial growth, 48 hours after the start of the treatment at a concentration of 4%. We conclude from these results and the variation that occurred in the times of inhibition and the concentration of the inhibitory substance that chlorhexidine is more effective than calcium hydroxide in its use as a mouthwash and treatment of bacteria present in the roots of the teeth.