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Background: Residual calculus exists not only on teeth treated by scaling alone but also on teeth treated by flap surgery. Periodontal microsurgery enables more definite removal of calculus, atraumatic handling of tissues through optical magnification. The purpose of this study was to compare the clinical outcomes of microsurgery with conventional open flap debridement in patients with chronic periodontitis. Materials and Methods: Thirteen chronic periodontitis patients were randomly assigned for test (microsurgical) and control (conventional) open flap debridement in a split mouth design. At baseline, 3, 6 and 9 months the following clinical parameters were recorded: Probing pocket depth, relative attachment level, gingival recession, gingival bleeding index. Postoperative healing at 1-week by early healing index and pain scale for 7 days were assessed. Results: Paired t-test was used to compare means within the groups, and unpaired t-test was applied to compare the means of the two groups. At 3, 6 and 9 months postoperatively there was a significant reduction in gingival bleeding index, probing pocket depth, relative attachment level within both the groups and there was no significant difference between both the groups. Gingival margin level and gingival recession increased in both the groups, but it was not statistically significant. Early healing Index score of 1 was found in 85% of test sites and 28% of control sites. The mean pain scale was 0 in test site and 1.07 ± 0.75 in control site. Conclusions: In open flap debridement procedure, a microsurgical approach can substantially improve the early healing index and induce less postoperative pain compared with applying a conventional macroscopic approach.