Antibiotics are generally an efficient means of treating bacterial infections, and therefore are an obvious candidate in the treatment of periodontal diseases. Systemically and locally administered antimicrobial agents of all kinds have been evaluated in multiple clinical trials. The vast majority of studies have tested antibiotics as adjuncts to non-surgical debridement. No regime has demonstrated superiority over systemically administered amoxicillin and metronidazole in the treatment of any clinically or microbiologically defined variant of periodontal disease. The frequency and consequences of adverse effects of antibiotics have always to be balanced against the potential consequences of not rapidly suppressing a periodontal infection. Proposed strategies to reduce the risk of bacterial antimicrobial resistance include: prescribing two drugs with a synergistic or complementary effect, the administration of antibiotics at a high dose for a short period, a combined approach with mechanical debridement to disrupt biofilms, and the focus on therapeutic rather than prophylactic use. Derivatives of existing antibiotic classes and new compounds that act on unique targets are the subject of preclinical investigations with a focus on action against antibiotic-resistant medical pathogens. In light of the excellent results of a combination therapy with well-established drugs that are cheap and efficient, clinical trials should compare newly proposed protocols for periodontal therapy to a positive control. Future studies should focus not only on the action against the microorganisms directly involved in periodontal diseases, but also on those relevant to other medical concerns.