Bacterial vaginosis (BV) is an enigmatic polymicrobial disease, and its evolution and pathobiology will not be solved by traditional culture-based methods. Characterization of the vaginal microbiota by polymerase chain reaction-based methods holds great promise. Molecular studies have identified species not detected by culture, but they also have missed some species identified by culture. These studies allow classification of both normal and BV patients based on distinct microbiologic profiles, which may prove important in accessing risk of BV, response to treatment, and risk of complications. More studies using new generations of primers and standardized methods are needed, and data must be analyzed after grouping patients according to microbiologic profiles.