Human beta-defensin-3 (HBD3), an endogenous antimicrobial peptide, has strong broad-spectrum antimicrobial activity. This study aimed to obtain recombinant HBD3 (rHBD3) and to test the hypothesis that the antimicrobial characteristics of HBD3 may offer an advantage over conventional medicine in reducing intracanal bacteria. Genetic engineering was used to obtain active rHBD3 and analysis revealed that it exhibited a broad spectrum of antibacterial activity at low micromolar concentrations against not only Staphylococcus aureus and Escherichia coli but also against some critical pathogenic microbes in infected root canals, including Fusobacterium nucleatum, Prevotella melaninogenica, Peptostreptococcus anaerobius, Streptococcus mutans, Actinomyces naeslundii, Enterococcus faecalis and Candida albicans. In an in vitro antibacterial experiment, rHBD3 significantly eliminated pathogenic bacteria in root canals. The ratio of bacterial death was up to 98%. We conclude that HBD3 has the potential to eliminate bacteria effectively and rapidly in the local microenvironment of the root canal system and that it may contribute to successful endodontic treatment.