Cationic antimicrobial peptides (AMPs) are among the best studied antimicrobial factors expressed in the respiratory tract. AMPs are released by epithelial cells and immune cells into the airway surface liquid covering the epithelial surfaces of the lung where they act as endogenous antibiotics. Plenty of studies showed that AMPs possess additional, often immunomodulatory functions besides their antimicrobial activities. AMPs are chemotactic for immune cells and modulate cellular mechanisms, such as proliferation of epithelial cells, epithelial regeneration, and angiogenesis. The expression and activity of AMPs are impacted by lung diseases and AMPs can have adverse effects in lung diseases. In this review, we discuss the regulation and functions of AMPs in host defense and respiratory tract diseases.