Antimicrobial peptides (AMP) produced throughout our body are important effectors in the defense barrier of innate immunity. Here, we have analyzed antimicrobial activity and polypeptide composition of meconium versus neonatal feces to address the development of antimicrobial defense of the neonatal gut. Extracts of meconium exhibited antimicrobial activity against Bacillus megaterium, Escherichia coli, and group B streptococci (GBS) but not against the yeast Candida albicans. Extracts of neonatal feces were found to possess low activity against E. coli, GBS, and C. albicans. However, the anti-B. megaterium activity was higher in the fecal extracts than in meconium. All activities were reduced or abolished when salt was added to the antimicrobial assay. The AMP cathelicidin LL-37, alpha-defensin HNP-1-2, alpha-defensin HD 5, and lysozyme were identified in both meconium and fecal extracts. In addition, HNP-3 and a fragment of azurocidin were found in meconium, whereas the holoprotein azurocidin was detected in feces. In meconium, histones H2A and H4 were isolated and identified by their antimicrobial activity. Notably, LL-37 and lysozyme were found at significantly higher levels in feces than in meconium. Our findings reveal that meconium and feces contain AMP, acting in the defense of the neonatal gut, and may be implicated in the control of the initial colonization.