The female reproductive tract is immunologically unique in its requirement for tolerance to allogeneic sperm and, in the upper tract, to the conceptus. However, it must also be appropriately protected from, and respond to, a diverse array of sexually transmitted pathogens. Some of these infections can be lethal (e.g. Human Immunodeficiency Virus (HIV), Human Papilloma Virus (HPV)), and others (e.g. Chlamydia trachomatis and Neisseria gonorrhoeae) can have potentially devastating reproductive sequelae. Interactions between a host and a pathogen are complex, diverse and regulated, and are a function of the individual pathogen, and host immunity. Although there is undoubtedly commonality in the mucosal immune response, there is also evidence of a degree of site-specificity in immune mechanisms, dependent upon the function and anatomical location of an organ. In this article, we review the evidence on the pivotal role of epithelial cells in the innate and early immune response to pathogen challenge in female genital tract tissues, and examine the evidence that the 'sterile' upper and the 'non-sterile' lower female genital tract may maintain a different immunological surveillance milieu, and may also respond differentially to pathogen challenge. We also review the unique characteristics, and subsequent ramifications of the acute cervical immune response to C. trachomatis, and discuss how natural antimicrobial mediators of immunity may be utilized to decrease the spread of sexually transmitted infections.