A large number of bioactive peptides derived from breast milk have been identified to be multifunctional having anti-inflammatory, immunoregulatory and antimicrobial activities. Here, we report that an endogenous peptide located at β-casein 211-225 amino acid from human breast milk (hereafter called CAMP211-225) presents specific antimicrobial activity against pathogenic E. coli and Y. enterocolitica. CAMP211-225 is a novel peptide that occurs at higher levels in preterm milk than in term milk. The minimal inhibitory concentrations (MIC) of CAMP211-225 against E. coli and Y. enterocolitica are 3.125 μg ml-1 and 6.25 μg ml-1, respectively, and the antimicrobial activity of CAMP211-225 was also confirmed by a disk diffusion assay. Further studies using fluorescence staining, scanning electron microscopy and a DNA-binding assay revealed that CAMP211-225 kills bacteria through a membrane-disrupting mechanism, but not by binding to intracellular nucleic acids. Neonatal necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease in neonatal intensive care units. In our study, CAMP211-225 administration effectively reduced ileal mucosa damage in an experimental NEC mice model. These results suggest that the antimicrobial peptide CAMP211-225 may have potential value in the prevention and treatment of neonatal infections.