Immune protection in the female reproductive tract (FRT) has evolved to meet the
challenges of sexually transmitted bacterial and viral pathogens, allogeneic spermatozoa, and an
immunologically distinct semi-allogeneic fetus. Throughout the FRT, the innate immune system is
essential for the recognition and initial response to incoming pathogens. Key mediators of innate
immune protection examined in this review include epithelial cells, stromal fibroblasts, macrophages,
DC, and neutrophils from the Fallopian tubes, uterus, cervix and vagina. These innate immune cells
respond to pathogens resulting in the secretion of cytokines, chemokines, antimicrobials, and
production of intracellular proteins that protect, activate and recruit both innate and adaptive immune
cells. Human immunodeficiency virus (HIV) infection can occur throughout the FRT, including the
ovary, and is modulated by multiple factors including age of the individual, epithelial barrier
integrity, composition of the vaginal microbiome, and hormonal status. Alterations in immune
function due to hormonal changes that optimize conditions for successful fertilization create a
hypothesized “window of vulnerability” that lasts from ovulation into the secretory stage of the
menstrual cycle. The goal of this review is to summarize the multiple levels of protection against HIV
infection in the FRT and thereby providing a foundation for the design of vaccines for protection
against sexually-transmitted infections (STI) including HIV.