Objective: To determine, 2 months post treatment,  if the adjunctive use of systemic amoxicillin and metronidazole during full-mouth non-surgical periodontal treatment performed within 24-hours (FPT) provided additional clinical improvements compared to FPT alone, in patients with generalized aggressive periodontitis (GAP).  Methods: 41 GAP patients were stratified for smoking habits and number of pockets ≥5mm and were randomly assigned to one of the treatment groups. 20 subjects in test  group (TG)  received  FPT  with adjunctive systemic amoxicillin (500mg/TID/7days) combined  with metronidazole (500mg/TID/7days). 21 subjects in placebo group (PG) received FPT with placebo medication. Oral hygiene and adverse events were evaluated at 1-5-9-weeks. Compliance with medication was recorded at 1-week. Clinical parameters were evaluated  by a calibrated blinded examiner  at baseline and 2-months, and a blinded therapist performed FPT. Results:  Both groups were balanced at baseline and all clinical parameters other than full-mouth plaque score showed improvement at 2 months. The improvement in full-mouth bleeding score for  TG was statistically significantly better than for PG (Mann-Whitney, P=0.017). Better probing pocket depth (PPD) reduction was achieved at TG compared to PG at  moderate (4-6mm) and deep pockets (≥7mm). The mean differences at PPD (4-6mm) was 1.2mm (95%C.I.: 0.9-1.5) in PG and 1.7mm (95%C.I.:1.5-1.9) in TG with a difference of 0.5mm between groups which was statistically significantly different (95%C.I.:0.2-0.7; ANCOVA, P=0.001). The mean difference at PPD ≥7mm was 2.1mm (95%C.I.:1.6-2.5) in PG and 3.0mm (2.6-3.3) in TG with a difference of  0.9mm  which was statistically significant (95%C.I.:0.4-1.4; ANCOVA, P=0.001). Mean Clinical attachment level gain in PPD≥7mm  was 1.3 (1.0-1.6) in PG and 1.8 (1.6-2.0) in TG with a difference of 0.5mm (95%C.I.:0.2-0.8; ANCOVA, P=0.002). Conclusions: Adjunctive use of systemic amoxicillin/metronidazole during FPT resulted in statistically significant additional improvements in the clinical conditions of GAP patients when compared to FPT alone  2 months  after treatment.