This paper describes steps in the process of evaluating subgingival bacteria assays for the diagnosis of periodontal disease. The first step examines the infectious etiology of periodontal disease in pointing to specific oral bacteria as periodontal pathogens. Second is characterization of the laboratory test to detect and quantitate these pathogens as to sensitivity, specificity, and positive and negative predictive value. Third is the role of the laboratory test in the diagnosis of the different forms of periodontal disease which is related to the current clinical rather than microbiological definition of these diseases. The fourth and most important step is an analysis of the significance of subgingival bacterial tests in clinical decision-making.