It has been established that the bacterial diversity in any given environment is severely underestimated when assessed by means of culture-based techniques. Yet, almost all currently available knowledge related to the periodontal microbiota in health and disease has been generated either by culture-based surveys or by methods that require prior species identification by culture. A handful of recent studies using culture-independent molecular methods providing 16S rRNA sequences for both cultivable and not yet cultivated species of human periodontal bacteria demonstrated a high bacterial diversity in the oral cavity. It has been estimated that approximately 500 species may colonize the human oral cavity, half of which have been cultivated to date. A review of the available epidemiological data on the prevalence of certain periodontal microbiota on a population level reveals considerable variation in estimates with respect to 1) sampling strategy, 2) mode of bacterial identification, and 3) race/ethnicity of the studied population. Nevertheless, specific bacterial profiles appear to confer high odds ratios for pathological periodontal conditions and/or progressive periodontal disease. However, the currently recognized periodontal pathogens are commonly recovered from periodontally healthy children, and their carrier rate in adults is substantial. Virulent clones, such as a highly leukotoxic strain of Actinobacillus actinomycetemcomitans, have been found to be closely associated with aggressive forms of periodontitis. In conclusion, while the majority of the periodontal microbiota are commensals, a subset of likely opportunistic pathogens fulfills the epidemiologic requirements needed in order to be ascribed as risk/causative factors. Given the large proportion of the periodontal microbial habitat that is currently insufficiently explored, and assuming that the hitherto uncultivated segment of the bacterial community will include similar levels of pathogenic species, the list of periodontal pathogens should be expected to expand.