Physical barrier function was formerly believed to play the major role in mucosal protection against luminal bacteria. This view has now been challenged by the discovery of specialized molecules that possess antimicrobial activity. More than 100 peptides have been identified so far, and the number is still growing. These peptides are distributed widely and conserved throughout phylogeny. The epithelial expression of antimicrobial peptides is of particular interest as many pathogens adhere to epithelial surfaces and may eventually invade the host. This rapidly acting defence system of innate immunity is already engaged before adoptive immune interactions take place. These antimicrobial peptides consist of constitutive and inducible forms, potentiating this barrier function in terms of an inflammatory response. One important subgroup of antimicrobial peptides is the family of defensins, which are classified as alpha (alpha-) and beta (beta-) defensins. Eight different peptides with varying antimicrobial properties have been identified. They are distributed widely in humans, and organ-specific expression patterns have been observed. Homologous peptides have been found in other mammals, vertebrates, invertebrates, insects and plants. The identification of alpha-defensins and their murine counterparts, cryptdins, in the small intestine prompted intensive research into epithelial antimicrobial defence.