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Objectives: To evaluate the comparative effect of 0.4 % Doxycycline gel and 1% Metronidazole gel as an adjunct to scaling and root planning in the treatment of chronic periodontitis. Study Design: Interventional study. Setting: Department of Periodontology at Isra Dental College, Isra University Hyderabad. Period: October 2017 to April 2018. Material & Methods: A sample of 60 patients of chronic Periodontitis were selected according to inclusion and exclusion criteria through non probability convenience sampling technique. Subjects were divided into 3 groups; GROUP A: Scaling and Root Planning (SRP) + 0.4 % doxycycline gel was applied sub-gingival, GROUP B: Scaling and root planning (SRP) + 1 % metronidazole gel was applied sub-gingival, GROUP C: Scaling and root planning (SRP) alone was performed. Data was recorded on proforma and was analyzed by using SPSS version 22.0. P value significance was taken ≤ or equal to 0.05. Results: Pocket depth at baseline in group A was 4.39± 0.20 which was reduced to 3.78± 0.53 and 3.30 ± 0.17 millimeters at day 10 and after one month respectively. Pocket depth at baseline in group B was 4.45± 0.19 which was reduced to 3.89± 0.51 and 3.34 ± 0.17 millimeters at day 10 and after one month respectively. Pocket depth at baseline is group C was 4.45± 0.18 which was reduced to 4.10± 0.20 and 4.06 ± 0.27 millimeters at day 10 and after one month respectively. Pocket depth at Day 10 in groups A, B and C showed statistically significant. Conclusion: Both Doxycycline and Metronidazole gel proved same efficacy when compared to control group. Since there is no difference in efficacy of doxycycline and metronidazole gels when applied in patients having periodontitis. [ABSTRACT FROM AUTHOR]