Background: Chlorhexidine has been extensively used in various periodontal and endodontic infections. However its use in combined endo perio lesion has not been defined clearly. The aim of this study was to evaluate the efficacy and synergistic effect of chlorhexidine intra canal medicament with combination of comprehensive periodontal therapy in endodontic periodontal lesions. 
 Materials and Methods: The patients were randomly assigned group 1 and group 2. Both the groups were treated by phase 1 and phase 2 periodontal treatments while group 1patients received conventional root canal treatment and group 2 patients were treated by chlorhexidine intracanal medicament for 6 months. The primary outcome measures are probing pocket depth, relative attachment level and bleeding on probing. 
 Results: Both groups showed improvement on primary outcome measures. However, group 2 showed significant more reduction in probing pocket depth (PPD) and bleeding on probing (BOP) and gain in relative attachment level (RAL) after complete 6 months treatment with chlorhexidine. Postoperative measurements from group1 and group 2 showed reductions in mean PPD of 2.63±0.98 and 3.57±1.13 mm, mean BOP reduction of 76.78±31.41and 87.54±22.35 and mean RAL gains of 2.42±1.27 and 3.42±0.94 mm, respectively. 
 Conclusion: 2% CHX gel used as an intracanal medicament along with periodontal treatment demonstrated more favourable treatment response in terms of periodontal healing.
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