Mucosal surfaces are often exploited as a portal of entry by a wide variety of microorganisms. An advanced understanding has been gained over the past decade of the immune system of the gastrointestinal and the respiratory mucosae. However, despite the fact that many viruses are transmitted sexually through the genital tract, the immune system of the male and female genital mucosae has received much less attention. Here, I describe and highlight differences of the innate and adaptive immune systems of the genital and intestinal mucosae, and discuss the challenges we face in the development of successful vaccines against sexually transmitted viral pathogens.