BACKGROUND AND OBJECTIVE: Pathogenic bacteria cause degeneration of periodontal tissues, which is essential for the reduction of gingival bacteria in order to reduce scaling and leveling. But there is no perfect treatment in pockets with a depth of more than 4 mm. Therefore, this study was conducted to investigate the effect of chlorhexidine gel as a topical supplementation after scaling and leveling the root surface in the treatment of moderate to advanced periodontitis. METHODS: This tripartite clinical trial was performed on 31 patients with chronic periodontitis, each with at least four pockets of depth of 4 to 6 mm. 62 areas as controls and 62 regions of the experimental group were selected randomly. In all patients, scaling and leveling of the root surface were done. In the experimental group, in addition to the scaling and leveling, the chlorhexidine gel surface was injected into the pockets. In four steps, before treatment, 2, 3 and 6 months after treatment, the clinical parameters of gingival index, bleeding index, plaque index, adhesion index and probe index depth index were measured and recorded. (IRCT:1R1N2013081314350). FINDINGS: The plaque index, bleeding index, gingival index and pocket probe depth in the group receiving the topical gel of chlorhexidine showed a significant difference in all levels of measurement compared to the control group (PI: control group was 2.75±0.44 and case group was 1.94±0.38, p=0.000, BI: The control group was 1.0±0.5, the case group was 0.05±0.44, p=0.000, PPD: the control group was 4.62±0.73, the case group was 3.88±0.83, p=0.000, GI: The control group was 1.77±0.42, case group was 1.18±0.18, p=0.000). CONCLUSION: The results showed that injection of chlorhexidine gel with scaling and leveling of the root surface resulted in a greater improvement in periodontal clinical indices than SRP alone.