Breast milk represents nature’s best mechanism to provide complete nourishment and protection to the newborn. Human breast milk acts as a store house of an array of bioactive factors, which includes antimicrobial proteins and antimicrobial peptides that confer early protection while lowering the incidence of developing various infections and exhibiting immune modulation property to activate the immune cells to fight against the invading pathogens. Among the bioactive peptides, endogenous peptides present in breast milk have opened a new window of research on studying their unique mechanisms of action. This will help in incorporating these peptides in formula milk for meeting special needs where breastfeeding is not possible. The present chapter aims to give a deep insight into the various antimicrobial peptides and the newly reported endogenous peptides in human breast milk with emphasis on their levels and activity in preterm milk as data related to this is lacking and preterm newborns are highly vulnerable to acquire infections. Further, the chapter focuses on highlighting the antibacterial mechanisms adopted by the bioactive peptides for protection against the neonatal bacterial pathogens with special emphasis on the infections caused by resistant bacterial strains in hospital settings (neonatal wards) and their future implications.