This study investigates the cyclic changes in innate immunity in the female reproductive tract (FRT) of mice during the estrous cycle. By examining uterine and vaginal tissues and secretions we show that innate immunity varies with the stage of the estrous cycle and site in the FRT. Secretions from the uterine lumen contained cytokines and chemokines that were significantly higher at proestrus and estrus relative to that measured at diestrus. In contrast, analysis of vaginal secretions indicated that only IL-1β and CXCL1/mouse KC changed during the cycle, with highest levels measured at diestrus and estrus. In contrast, vaginal α-defensin 2 and β-defensins 1-4 mRNA levels peaked at proestrus and estrus and are expressed 1-4 logs greater than that seen in the uterus. These studies further indicate that TLR5 and TLR12 in the uterus, and TLR1, TLR2, TLR5 and TLR13 in the vagina varies with stage of the estrous cycle, with some peaking at proestrus/estrus and others at diestrus. Overall, these studies indicate that innate immune parameters in the uterus and vagina are separate and discrete, and regulated precisely during the estrous cycle.