Background: The single most common primary etiological factor in periodontal disease is a bacterial plaque. Periodontitis affected root surface undergo physical and chemical damage that makes them a poor base for attachment and proliferation of fibroblast. Citric acid has a bacteriostatic effect and can cause root biomodification to remove the smear layer and expose root collagen fiber. Method: Forty swabs were taken from patients having periodontitis attended Al-Furat General hospital/ Dentistry department from August to November 2018. Each swab was taken around the tooth before and after tooth extraction. These swabs were cultured on blood and MacConkey agar plates. Different types of bacteria were isolated in the area of periodontitis. In addition, different concentrations of citric acid solution (0.3, 0.4, 0.5, 0.75 and 1 g/ml) were prepared and added to bacterial growth, and then the minimum inhibition zone was determined. Results: Four types of bacteria were isolated from the patient in the area of periodontitis: Streptococcus mutans, Escherichia coli, Staphylococcus aureus and anaerobic bacteria. No bacteria were isolated in the area after tooth extraction. Concentrations of the citric acid that showed the zone of inhibition on bacterial growth were 0.4, 0.5, 0.75, and 1 g/ml. Conclusion: Streptococcus mutans appeared at a high level in patients with periodontitis. The concentration of citric acid (0.4, 0.5, 0.75, 1 g/ml) was proved to inhibit the growth of bacteria in the smear area of diseased teeth; therefore, could be suggested to be used as a root conditioning agent.