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Aggressive periodontitis is characterized by a considerable attachment loss over a relatively short period of time. It may be the consequence of either the presence of highly aggressive pathogens or a highly susceptible host. In the first case, the use of antimicrobials should be beneficial in the treatment of those patients. However, due to the organization of the micro-organisms as a biofilm, the increasing incidence of allergies and resistance against antimicrobials and their side-effects, there is still controversy about their benefit in the treatment of periodontal disease. This paper discusses indications for the use of antimicrobials, the substances prescribed and the type of application under the conditions of aggressive periodontitis.