This paper summarizes the rationale for the application of microbiology in the management of destructive periodontal diseases. The subgingival microbiota in patients with severe periodontitis is complex and contains high numbers of obligate anaerobic bacteria as well as facultative micro-organisms. It has become clear that major differences exist in the composition of the subgingival microflora. These differences are not only quantitative but also qualitative. Difference in plaque composition is the basis for the application of clinical microbiology in the management of periodontal disease. Several bacterial species have emerged as useful indicators for progressive periodontitis. In this respect, the importance of Actinobacillus actinomycetemcomitans, Bacteroides gingivalis and Bacteroides intermedius has been shown in a number of studies. It has become clear that A. actinomycetemcomitans is not specifically associated with the local form of juvenile periodontitis, but this micro-organism is probably also of importance in severe periodontitis in adult patients. Selection of individuals with an A. actinomycetemcomitans associated periodontitis is essential since successful treatment in these patients needs an adjunctive antibiotic therapy. Microbiological testing can be useful in patients showing a poor response to periodontal treatment (refractory periodontitis). Factors which may be responsible include poor oral hygiene, poor subgingival debridement, the patient's susceptibility and a subgingival microflora resistant to therapy. In this patient category, microbiological testing is capable of diverting continuing periodontal treatment. Furthermore, microbiology can be useful in evaluating periodontal treatment. Successful elimination of specific periodontopathic microorganisms can be used to determine recall intervals.