The oral microbiota plays a primary role in the initiation and progression of the most common forms of periodontal disease. Because of the multiplicity of factors that control the establishment and long-term evolution of the oral microbiota, a great deal of heterogeneity exists in the composition of the periodontal microbiota among individual subjects. Despite these individual differences and the complex interactions between bacteria and the host and among bacteria, an association has been demonstrated between certain species and various forms of periodontal disease. However, the predictive value of either positive or negative tests for selected bacterial species has not proved to be high enough for routine use in clinical practice. Nevertheless, bacteriological tests have been of value in the management of patients with juvenile periodontitis and refractory forms of periodontal disease. The increasing availability of diagnostic laboratory services and diagnostic kits for office use will make it easier for the practitioner to select appropriate antimicrobial treatments and monitor patients undergoing antimicrobial therapy.