Antimicrobial peptides (AMPs) protect the epithelia of mucosal organs like the respiratory or the gastrointestinal tract from invading microorganisms. As an integral part of the innate immune system they display antimicrobial activity against gram- and gram-negative bacteria as well as against fungi and enveloped and non-enveloped viruses. Besides their microbicidal effects they have important functions in the regulation of repair and inflammation. AMPs are sometimes referred to as 'alarmins' due to their ability to recruit, modulate and activate components of the immune system. In contrast, some AMPs suppress activation of the immune system. AMPs are also involved in tissue repair, cancer biology and angiogenesis. Based on their antimicrobial and immunomodulatoy functions, AMPs are probably involved in the pathogenesis of infectious and inflammatory diseases of the lung. Inborn or acquired deficiencies contribute to susceptibility to infection and colonisation. The potential pro-inflammatory role of AMPs contributes to the disease processes in inflammatory disorders such as asthma, chronic obstructive pulmonary disease, sepsis or pulmonary fibrosis. This review summarises the knowledge about the functions of AMPs in the pulmonary innate host defence system and their role in respiratory disease.