The mucosal surfaces of the gastrointestinal tract are continually exposed to an enormous antigenic load of microbial and dietary origin, yet homeostasis is maintained. Pattern recognition molecules (PRMs) have a key role in maintaining the integrity of the epithelial barrier and in promoting maturation of the mucosal immune system. Commensal bacteria modulate the expression of a broad range of genes involved in maintaining epithelial integrity, inflammatory responses, and production of antimicrobial peptides. Mice deficient in PRMs can develop intestinal inflammation, which is dependent on the microbiota, and in humans, PRM polymorphisms are associated with exacerbated inflammatory bowel disease. Innate immune responses and epithelial barrier function are regulated by PRM-induced signaling at multiple levels, from the selective expression of receptors on mucosal cells or compartments to the expression of negative regulators. Here, we describe recent advances in our understanding of innate signaling pathways, particularly by Toll-like receptors and nucleotide-binding domain and leucine-rich repeat containing receptors at mucosal surfaces.