Antimicrobial peptides are cationic molecules, which participate in multiple aspects of the immune response including the control of inflammatory diseases, characteristic that make these molecules attractive as therapeutic tools. These peptides are produced in bacteria, insects, plants and vertebrates, and are classified together due to their capacity to directly inhibit the growth of microorganisms, and to regulate the immune response by inducing the secretion of chemokines and cytokines. Various families of antimicrobial peptides have been identified including the cathelicidins and defensins, the most investigated human antimicrobial peptides. This review will cover the main biological functions of antimicrobial and cell-penetrating peptides in inflammation, and describe the importance and utility of antimicrobial peptides as therapeutics for inflammatory diseases.