Mucosal surfaces are continually exposed to a wide range of potentially pathogenic organisms, yet the incidence of infectious disease resulting from these encounters is relatively low. This suggests the presence of highly effective defence mechanisms in these tissues. Antimicrobial peptides have recently been discovered in mucosal tissues and may play a significant role in host defence. Several mucosal peptides (andropin, magainin, tracheal antimicrobial peptide, enteric defensins and PR-39) all fulfil minimal criteria for a role in mucosal host defence, including potent in vitro antimicrobial activity and accumulation at the mucosal surface. Most of these mucosal peptides are encoded by members of large gene families that contain members found in other biological contexts more classically associated with antimicrobial defence. The abundance, activity and evolutionary history of several epithelial peptides suggest that antimicrobial peptides play a key role in host defence at mucosal surfaces.