It is common practice to carry out the therapy of periodontal diseases in two phases. In a first, non-surgical phase, bacterial deposits on tooth surfaces (plaque and calculus) are removed using a cleaning method called "scaling and root planing" (SRP). After three to six months the case is evaluated and, if necessary, further treatment is provided, usually taking a more aggressive, surgical approach. Beneficial effects of adjunctive systemic antibiotics on clinical outcomes have been shown repeatedly but specific indications for antibiotics in subgroups of diseased patients, and the optimal timing of antimicrobial therapy, continue to be issues of a long lasting controversy.This study assessed the differential outcomes of periodontal therapy supplemented with amoxicillin-metronidazole during either the non-surgical or the surgical treatment phase.