Background: Antibiotics are known to improve clinical parameters in patients with periodontitis, so they should be capable of enhancing the surgical treatment outcome by improving clinical parameters when given adjunctively following periodontal flap surgery. Methods: Thirty subjects with moderate to severe periodontitis were randomly divided into three groups: Group I: 10 patients without antibiotic prescription after flap surgery, Group II: 10 patients prescribed with metronidazole 400 mg t.i.d. for 14 days, and Group III: 10 patients prescribed with doxycycline 200 mg o.d. as booster dose followed by successive doses of 100 mg o.d. for 21 days. Plaque index (PI), gingival index (GI), pocket probing depth (PPD), and clinical attachment level (CAL) were recorded at baseline, 2 weeks, and 2 months. The mean values and standard deviation values for each parameter were calculated using analysis of variance. Group comparison was done using paired t -and unpaired t -tests. Results: Reduction in PI, GI, PPD, and CAL after 2 weeks and 3 months from baseline in all the three groups was seen; intergroup comparison showed more reduction in PPD and GI and more gain in CAL in Groups II and III after 3 months when compared with Group I. No statistical difference was seen between Groups II and III. Conclusion: Within the limits of this study, it can be concluded that antibiotic administration as an adjunct to conventional flap surgery helps in improving clinical parameters.