A gene expression system for antimicrobial peptides, which could be effectively used for various studies or applications of the antimicrobial peptides, has been developed. To avoid the harmful effects on an expression host, Escherichia coli, the antimicrobial peptides were expressed as fusion proteins with a polypeptide F4, which is a truncated PurF fragment that highly tends to form inclusion bodies. Seven different kinds of antimicrobial peptides have been successfully expressed by this expression system and the resulting expression level of fusion proteins reached up to 30% of total cell proteins. To confirm the identity of the recombinant peptide, MSI-344 was selected as a model peptide and purified to homogeneity, and we could obtain the recombinant MSI-344 of a high purity and with a good yield, which was identical to the authentic peptide in the aspects of the chemical and antimicrobial properties. These results show that the neutral fusion partner, which reinforces the formation of inclusion bodies, could mediate a high-level expression of the antimicrobial peptides.