To our knowledge, no data are available on whether the microbial species composition and abundance sampled with self-collected vaginal swabs are comparable to those of swabs collected by clinicians. Twenty healthy women were recruited to the study during a routine gynecological visit. Eligible women were between 18 and 40 years old with regular menstrual cycles. Participants self-collected a vaginal swab using a standardized protocol and then were examined by a physician, who collected an additional five swabs from the lateral wall of the mid-vagina. In this study, the self-collected and three physician-obtained swabs were analyzed and compared using terminal restriction fragment length polymorphism and sequence analyses of the 16S rRNA genes. Vaginal microbial community comparative statistical analyses of both T-RFLP and 16S rRNA gene sequence datasets revealed that self-collected vaginal swabs sampled the same microbial diversity as physician collected swabs of the mid-vagina. These findings enable large-scale, field-based studies of the vaginal microbiome.In recent years, "cultivation-independent" methods based on the analysis of 16S rRNA gene sequences directly extracted from biological samples are widely used to explore microbial diversity in various habitats (7,27,28). Using these methods, organisms are classified based on phylogenetic differences that are reflected in sequence polymorphisms of their 16S rRNA genes. The use of these approaches obviates the need to cultivate organisms, permits high-throughput analysis of samples, and provides precise and detailed information about the populations present. Using 16S rRNA gene analysis, the species (phylotype) composition and abundance in microbial communities can be readily determined, and similarities and differences among microbial communities can be quantitatively discerned. Despite difficulties in comparing data generated by different so-called "universal" PCR primer pairs, each introducing small biases (8, 36), this validated method has become the favored approach to characterizing the mutualistic microbial populations residing on and in the human body, including the gastrointestinal tract (4, 37), skin (4, 10), subgingival crevice (19), and vagina (4, 9, 15, 42). Importantly, the data obtained can be statistically analyzed to test the significance of changes that occur within individuals over time, or between individuals and treatment groups. These methods include terminal restriction fragment length polymorphisms (T-RFLP) (41) and high-throughput pyrosequencing of bar-coded 16S rRNA gene analysis (12,22).Surveys of vaginal microbial communities using cultivationindependent methods have been initiated under the NIH Roadmap Human Microbiome Project (14). Surveys of the vagina are important for a number of reasons. The beneficial effects of the endogenous microbiota on women's health in obstetric and gynecologic outcomes are numerous but poorly understood. A proper understanding of community membership, relative abundance, and variations therein are crit...