Under normal circumstances, the vagina is home to many different microorganisms. A shift in the balance of vaginal microbiota can result in infections such as bacterial vaginosis (BV), the most common cause of vaginal infection. BV and other infections are associated with early pregnancy loss, preterm labour, and an increased risk for HIV. Our primitive understanding of the complex microbial ecosystem of the genital tract greatly hampers our ability to identify and describe normal vaginal microbiota. This hinders the development and evaluation of appropriate, focused therapies for genital infections. The use of high throughput molecular methods promises to be very effective for characterizing vaginal microbiota. This award supports the development of a multidisciplinary, team of researchers, with links across Canada, to apply molecular methods for microbial species identification. Their comprehensive description and monitoring of vaginal microbiota will facilitate the development of new diagnostic technologies and therapies for infection-related problems in obstetrics and gynecology.