Background: Orthodontic treatment can be an uncomfortable experience. Two to three weeks after plaque accumulation, white spot lesions appear on the buccogingival areas and may lead to patient dissatisfaction at the end of orthodontic treatment. Hence; the present study was undertaken for comparing the effect of two different antiplaque agents on patients undergoing fixed orthodontic treatment. Materials & methods: A total of 20 patients scheduled to undergo fixed orthodontic treatment were enrolled in the present study. All the patients were broadly divided into two study groups with 10 patients in each group. In one group, Chlorhexidine gel was used (CLX Group) and in other group, metronidazole gel was used (MTZ Group). Mean probing depth and mean gingival index was assessed in both the study groups at initial time, 6 weeks during treatment and 12 weeks during treatment. All the results were recorded in Microsoft excel and were analysed by SPSS software. Results: Mean probing depth among subjects of CLX group at baseline, 6 weeks and 12 weeks was found to be 4.3, 2.2 and 2.1 respectively. Mean probing depth among subjects of CLX group at baseline, 6 weeks and 12 weeks was found to be 4.4, 2.3 and 2.0 respectively. While comparing mean probing depth in between the two study groups at different time intervals, non-significant results were obtained. Also, while comparing the mean gingival index in between the two study groups, non-significant results were obtained. Conclusion: Both chlorhexidine gel and metronidazole gel can be used with equal effectiveness in patients undergoing orthodontic treatment.