The vagina is a dynamic system that is sterile at birth but becomes colonized within a few days with predominantly gram-positive organisms, including anaerobes,Staphylococcus, Streptococcus, and diphtheroids. Before menarche the vaginal pH is near neutral (pH 7.0). At puberty the vaginal ecosystem changes, fueled by hormonal changes, which results in a natural defense system for the lower genital tract. Estrogen causes the vaginal epithelium to thicken, glycogen levels to rise, and cervical mucus to increase. The predominant flora change to lactobacilli whose morphology is large straight or curved rods.

In fact, in a normal woman with adequate levels of estrogen, lactobacilli make up greater than 95% of microorganisms present in the vagina. This organism metabolizes glycogen to lactic acid and hydrogen peroxide (H₂O₂), resulting in a drop in vaginal pH to <4.5. The low vaginal pH produces an environment that is hostile to other microorganisms while favoring growth of lactobacilli. Lactobacillus also interferes with bacterial adhesion to epithelial cells and competes effectively for nutrients. The low pH is maintained in a healthy vagina until menopause, when because of waning estrogen levels, the vaginal epithelium thins, and a mixed flora returns with increasing levels of anaerobes and decreasing levels of lactobacilli. The result is a vaginal pH that rises to above 6.0 in the postmenopausal state.