Aim: To evaluate the effect of systemic Amoxycillin and Metronidazole against Azithromycin as an adjunct to non-surgical therapy and correlate the clinical periodontal parameters at baseline, 10 days and 30 days in subjects with generalized aggressive periodontitis (GAP). Study Design: Randomized controlled clinical trial. Place and Duration of the Study: The study was conducted in Saveetha Dental College and Hospitals from February 2015 to August 2015. Methods: Subjects were recruited from the outpatient department of Periodontics and were categorized as GAP according to AAP criteria. A total of 16 patients with GAP were included in the study. Clinical periodontal parameters like sulcus bleeding index [SBI], gingival index [GI], Probing depth [PD] and clinical attachment loss [CAL] were recorded at baseline. The subjects were then randomly allotted into Group 1 [Amoxycillin+Metronidazole] and Group II [Azithromycin]. After evaluation of clinical parameters at baseline, scaling and root planning [SRP] was done in both the Groups and systemic antibiotics, namely combination of Amoxycillin and Metronidazole in Group I and Azithromycin in Group II were administered. Subjects were recalled at day 10 and 30 for re-evaluation of clinical parameters. Within Group comparison was made using paired “t test” and inter Group comparison was made using Un-paired “t test”. Results: Intra-Group comparisons of clinical parameters between baseline and 30 days, in both the Groups were statistically significant (P 0.05). Conclusion: Systemic administration of Azithromycin as an adjunct to SRP in subjects with GAP resulted in better improvement of clinical periodontal parameters compared to a combination of Amoxycillin and Metronidazole.