The use of non-culture gene amplification techniques has improved our understanding of the composition of the vaginal bacterial ecosystem. In most healthy women in the reproductive period the predominant vaginal bacteria are one or more of the following species of Lactobacillus: L. crispatus, L. iners and L. gasseri. However, in other apparently healthy women lactobacilli may be deficient or absent, being replaced by other lactic-acid-producing bacteria: Atopobium, Megasphaera and/or Leptotrichia species. Infection and/or proliferation of pathogenic bacteria in the vagina is suppressed by lactic acid production, bacteria-generated antimicrobial products, and the local activities of the innate and cell-mediated immune systems. Vaginal epithelial cells produce a range of compounds with antimicrobial activities. These cells also possess membrane-bound Toll-like receptors that recognize pathogen-associated molecular patterns. Recognition leads to pro-inflammatory cytokine production and antigen-specific immunity. Local production of IgG and IgA antibodies can also be initiated in the endocervix and vagina in response to infection.