Antimicrobial peptides or host defence peptides are endogenous peptide antibiotics, which have been confirmed as an essential part of the immune system. Apart from direct killing of bacteria, a role for the peptides in antiviral and immunomodulatory functions has recently been claimed. In this chapter we have focused on the host contact with microbes, where these host defence peptides are key players. The interplay with commensals and pathogens in relation to antimicrobial peptide expression is discussed, with specific emphasis on the respiratory and the alimentary systems. A possible novel difference in epithelial interactions between commensals and pathogens is considered in relation to disease.