Explorations of the vaginal microbiota (VMB) began over 150 years ago. Using light microscopy and bacterial cultures, the concept of normal versus abnormal microbiota in women began to emerge. The latter became known by the term "bacterial vaginosis" (BV). BV microbiota is dominated by Gardnerella vaginalis and includes a number of anaerobic organisms. In contrast, normal flora is dominated by various Lactobacilli. BV microbiota is associated with vaginal discharge, poor pregnancy outcomes, pelvic inflammatory disease, postoperative wound infections and endometritis after elective abortions. In addition, BV flora predisposes women to infection by human immunodeficiency virus and sexually transmitted diseases. Application of molecular techniques over the past decade has significantly advanced our understanding of the VMB. It is far more complex than previously recognized and is composed of many previously unknown organisms in addition to those already identified by culture. Analyses using high-throughput sequencing techniques have revealed unique microbial communities not previously recognized within the older, established vaginal flora categories. These new findings will inform the design of future clinical investigations of the role of the VMB in health and disease.