The present paper describes the use of oral antibiotics in the treatment of severe periodontitis based on the composition of the subgingival flora. Antimicrobial therapy is applied within the concept of the three basic steps in periodontal treatment. It is demonstrated in the literature that the use of antibiotics based on clinical and microbiological parameters, can reduce the need of periodontal access surgery. Proper infection control is also related to favourable outcome of regenerative periodontal procedures and periodontal plastic surgery. Therefore, the proper use of antibiotics may result in a shift in indication for different modalities of periodontal surgery.