Endogenous antimicrobial peptides (AMPs)mediate innate immunity in every species in which they have been investigated. Cathelicidins and defensins are the two major AMP families in mammals, and they are abundant components of phagocytic leukocytes and are released by epithelial cells at mucosal surfaces. In the small intestine, Paneth cells at the base of the crypts of Lieberkühn secrete α-defensins and additional AMPs at high levels in response to cholinergic stimulation and when exposed to bacterial antigens. Paneth cell α-defensins evolved to function in the extracellular environment with broad-spectrum antimicrobial activities, and they constitute the majority of bactericidal peptide activity secreted by Paneth cells. The release of Paneth cell products into the crypt lumen is inferred to protect mitotically active crypt cells from colonization by potential pathogens and confers protection from enteric infection, as is evident from the immunity of mice expressing a human Paneth cell α-defensin transgene to oral infection by Salmonella enterica serovar Typhimurium. α-Defensins in Paneth cell secretions also may interact with bacteria in the intestinal lumen above the crypt-villus boundary and influence the composition of the enteric microbial flora. Mutations that cause defects in the activation, secretion, dissolution, and bactericidal effects of Paneth cell AMPs may alter crypt innate immunity and contribute to immunopathology.