Statement of Problem: The primary treatment of chronic periodontitis is scaling and root planning (SRP). In deep pockets, surgery is recommended following primary treatment. It has been claimed that local delivery devices can improve healing of inflammation.Purpose: The purpose of this study was to compare the efficacy of adjunctive use of subgingival minocycline application in periodontal pockets in patients after SRP with those treated only by SRP.Materials and Method: This study was performed on fifteen patients with probing depth of 5mm or more. Probing depth, clinical attachment level, plaque index and bleeding index were evaluated at base line, and then primary treatment (SRP) was performed in all patients. In every patient one tooth was selected as experimental and one as control. In pockets of the test teeth, minocycline gel 2% was applied in weeks 0, 2, 4 and then were compared with control teeth in weeks 2, 4, 16 which received only SRP treatment. For statistical analysis paired t-test and student t-test were utilized. Results: The mean of probing depth at base line, and 16th weeks in experimental group, was 6.530.83 and 3.460.76, while in control group it was 6.330.83 and 4.300.75 respectively. Pocket depth reduction in experimental group was more significant ( p<0.001).The attachment level in experimental group at base line, and 16th weeks was 0.650.14 and 1.660.36 and in control group it was 0.780.16 and 1.330.36. The increased level of attachment in experimental group was more significant ( p<0.001). The Bleeding and plaque Index also reduced in both group but they were more significant in experimental group ( p<0.001).Conclusion: In this clinical trial, the results suggest that SRP with adjunctive subgingival administration of minocycline gel is more effective compared to SRP alone. This may be related to good access and high concentration of drug in the area.Key words: Periodontitis. Drug therapy. Minocycline.