The female and male reproductive tracts are complex eco-systems where immune cells, hormones, and microorganisms interact. The characteristics of the reproductive tract mucosa are distinct from other mucosal sites. Reproductive tract mucosal immune responses are compartmentalized, unique, and affected by resident bacterial communities and sex hormones. The female and male genital microbiomes are complex environments that fluctuate in response to external and host-associated stimuli. The female vaginal microbiota play an important role in preventing colonization by pathogenic organisms. Sex hormones and their duration of exposure affect the composition and stability of the microbiome as well as systemic and mucosal immune responses. In addition to the characteristics of the pathogen they are targeting, successful vaccines against sexually transmitted pathogens must take into account the differences between the systemic and mucosal immune responses, the compartmentalization of the mucosal immune responses, the unique characteristics of the reproductive tract mucosa, the role of the mucosal bacterial communities, the impact of sex hormones, and the interactions among all of these factors.