The antimicrobial peptide is one of major effectors of the innate immunity, and is common in the entire multicellular organisms. In mammals, one family of antibacterial peptide named defensins plays a central role in host defense, especially in the epithelial surface such as oral cavity, skin and the intestine. Recently, the importance of the antimicrobial peptides has been widely recognized. The epithelium of the gut is a largest surface that is exposed to various pathogens in the environment. It is the Paneth cells that produce antimicrobial peptides, α-defensins in the small intestine. Paneth cells contribute to mucosal innate immunity by sensing bacteria and releasing microbicidal activities mostly from activated α-defensins. In mice, α-defensins, named cryptdins, consisted of six major isoforms (cryptdin-1 to cryptdin-6), and among those cryptdin-4 is the most microbicidal, suggesting that cryptdin-4 has a pivotal role in innate immunity. Paneth cell α-defensins have selective activities against commensal bacteria which may be associated with compositions of intestinal microbiota in vivo and homeostasis of the entire intestine. In addition, Paneth cell α-defensins appeared to be regulated topographically to control intestinal integrity.