The aim of the study was to investigate the effect of surgical therapy combined with the usage of metronidazole gel in the treatment of juvenile periodontitis by comparing clinical indices of flap operation along with application of metronidazole gel and flap operation only. Comparing clinical indices of the baseline, 3 months after surgery, 6 months after surgery statistically, the results are as follows; 1. Bleeding on probing (BOP) was decreased significantly both in the experimental group and the control group at 3 months after surgery (p<0.05). BOP increased 0.9% in the control group 6 months after surgery, while in the experimental group, decreased 4.7% (p>0.05). However, there was no statistically significant difference in these groups (p>0.05). 2. Pocket probing depth (PPD) was decreased significantly both in the experimental group and the control group at 3 months after surgery (p<0.05). PPD increased 0.lmm in the control group 6 months after surgery, while in the experimental group, no increase of the depth could be observed (p>0.05). However, there was no statistically significant and difference in these groups (p>0.05). 3. Loss of attachment level(LOA) was decreased significantly both in the experimental group and the control group at 3 months after surgery (p<0.05). LOA increased 0.2mm in the control group 6 months after surgery, while in the experimental group, increased 0.3mm However, there was no statistically significant difference in these groups (p>0.05). In conclusion, flap operation was effective on the treatment of juvenile periodontitis. However, combined therapy of metronidazole gel could not give rise to any significant adjunctive effect on the treatment outcome.