Resistin-like molecule beta (RELMβ) is a small cysteine-rich protein secreted by colonic epithelial cells. RELMβ mRNA and protein expressions are dramatically induced by bacterial exposure in germ-free mice. We hypothesized that RELMβ has antimicrobial activity. The antimicrobial activity of RELMβ was screened by an agar spot test and confirmed by a liquid broth test. The amount of RELMβ in human stools was semi-quantified by Western blot analysis. The induction of RELMβ mRNA and protein expression by bacteria was measured by quantitative RT-PCR using LS174T cells. Electron microscopic immunohistochemistry was performed using polyclonal anti-RELMβ antibody. RELMβ showed antimicrobial activity against S. aureus and all MRSAs examined in a dose- and pH-dependent fashion. Western blot study showed that the amount of RELMβ in healthy human stools was comparable to that exhibiting antimicrobial activity in vitro. Both RELMβ mRNA and protein expression were induced by heat-inactivated S. aureus, but not by E. coli in LS174T cells. Electron microscopic immunohistochemistry showed that RELMβ bound to the cell surface of S. aureus, followed by destruction of the bacterial cytoplasm. RELMβ is a colonic antimicrobial protein and its antibacterial activity is species selective. Because RELMβ is abundant in healthy human stool, RELMβ may modulate gut flora.