Bacterial vaginosis (BV) has been associated with severe medical consequences including induction of preterm birth and increasing susceptibility to infection by HIV and other genital tract pathogens. Although the mechanism by which BV induces these changes is not yet fully defined, the presence of BV is accompanied by immunologic changes in the lower genital tract environment. The most striking change is the induction of higher levels of proinflammatory cytokines, although this is not accompanied by increased levels of neutrophils. Increased cytokine levels are likely induced by bacterial products present in BV through innate immune recognition pathways such as the toll-like receptors. Recent studies show that changes in HIV susceptibility and HIV detection are associated with changes in bacterial flora. Further research is needed to identify the relative contributions of immune pathways and bacterial flora toward the pathogenic alterations that occur in BV.