Background Human β-defensin-3 (HBD3) is an epithelial peptide that has been demonstrated to have a salt-insensitive broad spectrum of potent antimicrobial activity. Expressing antimicrobial peptides in Escherichia coli (E. coli) is very difficult for it can result in death of the bacterial host cells. Our aim was to establish a prokaryotic system expressing soluble HBD3 protein and demonstrate the antimicrobial activity of the expressed protein. We then studied whether the host cells would activate the suicide pathways.Methods We first cloned the complementary DNA coding for the mature chain of HBD3, inserted it into the vector PGEX-KG then transformed E. coli BL21 (DE3) with the appropriate recombinant plasmid. After induction with 0.5 mmol/L isopropyl-1-thio-β-D-galactopyranoside (IPTG) the transformed E. coli produced a recombinant glutathione S-transferase and HBD3 (GST-HBD3) fusion protein. The fusion protein was treated with thrombin to produce pure HBD3 protein then the antimicrobial activity of HBD3 was evaluated in a liquid microdilution assay.Results The fusion protein GST-HBD3 was efficiently cleaved by thrombin and yielded HBD3 that had anti-staphylococcus aureus activity with a minimal inhibitory concentration level of 12.5 μg/ml. The E. coli strain expressing the recombinant protein did not grow slower than the empty vector strain.Conclusion Active HBD3 in E. coli by expressing the recombinant protein GST-HBD3 could be produced, and suicide did not occur in the E. colistrain expressing the recombinant protein.