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Antimicrobial peptides (AMPs) have evolved through billions of years as part of our innate immune system. These agents are produced by various cells throughout the human body and play important roles in our ability to respond to infections. In this review, we outline evidence linking AMP expression with a range of inflammatory and autoimmune human diseases. Finally, we highlight the promise of endogenous AMP induction for the treatment of disease (i.e., host-directed therapy) and briefly mention the different peptide drugs that are currently undergoing clinical trials.