Recent increase of antibiotic-resistant pathogens demands exploration of novel antimicrobial molecules with unexploited mechanisms. Several hundred host defense peptides have been isolated from natural sources and their functions characterized. As host defense peptides have several advantages over classic antibiotics for resistant pathogens, there are many efforts to develop host defense peptides as therapeutic agents. In this review, focusing on the development of short antimicrobial peptides (≤18-mer), several examples are introduced that identify the active fragment from cyclic host peptides, or novel antimicrobial peptides derived from combinatorial libraries. Moreover, structure-activity relationships of short antimicrobial peptides are discussed, and several methods for improving bioavailability as well as specificity of the peptides, such as D-amino acid replacements, unnatural amino acid replacements, and backbone modifications, are discussed.