Knowledge of the abundance of bacterial species in vaginal communities will help us to better understand their role in health and disease. However, progress in this field has been limited because quantifying bacteria in natural specimens is an arduous process. We developed quantitative real-time PCR (qPCR) assays to facilitate assessments of bacterial abundance in vaginal specimens and evaluated the utility of these assays by measuring species abundance in patients whose vaginal floras were clinically described as normal, intermediate, or bacterial vaginosis (BV) as defined by Nugent's criteria. The qPCR measurements showed that Lactobacillus species were predominant in normal vaginal specimens and that high Lactobacillus crispatus and Lactobacillus jensenii abundance was specific to normal specimens, while Lactobacillus iners abundance was high in all categories including BV. The abundances of all non-Lactobacillus species were higher in BV specimens than in normal specimens. Prevotella species were prevalent in all specimens and represented a high percentage of total species in BV specimens. qPCR assays can be a useful tool for describing the structure of vaginal communities and elucidating their role in health and disease.Vaginal bacterial communities are composed of mixtures of diverse species, and the relative abundance of these species in part determines urogenital health and disease in women (22). It is generally acknowledged that vaginal communities predominated by Lactobacillus species are normal and healthy while communities predominated by other genera, such as Gardnerella vaginalis, are abnormal and unhealthy (36). The latter condition essentially defines a poorly understood syndrome known as bacterial vaginosis (BV). While BV can be asymptomatic and benign in some women, it is a common cause of malodorous vaginal discharge for many. Moreover, BV flora is of concern because it is associated with an increased risk of adverse sequelae, such as preterm birth (8, 24), postoperative complications in women (40), enhanced risk of acquiring sexually transmitted infections (31), and increased shedding of HIV (11). Treating BV has not proven effective for the prevention of these adverse events possibly due to the fact that standard BV treatment results in high failure and relapse rates (25,29). Furthermore, while suspected pathogens such as G. vaginalis have been implicated, no agent or factor has been identified as the cause of BV, despite experimental (10) and epidemiological (28) evidence that suggests that BV is transmissible (10). Because of all the uncertainties surrounding this syndrome, BV has been described as a microbiological and clinical enigma (16,17).Failure to understand the microbiology specific to BV is perhaps not surprising given that the basic ecology of the genitourinary microbiota, namely, the composition, relative abundance, and temporal fluctuations of vaginal species, are poorly understood. This lack of knowledge is highlighted by recent cultivation-independent broad-range PCR surveys,...