The innate immune system oversees the gateway to immunity with its microbial sensors. Innate microbial sensors are germ line-encoded receptors with genetically predetermined specificities for microbes. The readiness and effectiveness of the innate immune system to provide immediate and appropriate responses at the host-environment interface is dependent on its sensitive and comprehensive microbial detection systems. The purpose of this review is to provide an overview of innate microbial sensors, our growing understanding of their diverse repertoire, and their elegant structural and functional approaches to microbial recognition. Their relevance to allergic disease is also discussed: the potential recognition and uptake of allergens by some of these receptors, inhibited expression of other microbial sensors by allergic immune responses and inflammation, and their upregulation by microbial exposures in early life that may help to protect against the development of allergic immune responses and disease.