Probiotics are specific microbes that, when consumed, contribute to the management of disease or to reducing the risk of disease. Probiotic bacteria have been shown to have several effects that might be of benefit to the neonate, including: modulating the establishment of intestinal microbiota, degrading antigens, promoting mucosal barrier functions and inhibiting mucosal pathogen adherence, and enhancing the maturation of the innate and adaptive immune systems. Results from clinical trials suggest that specific probiotics might be useful in reducing the risk of necrotising enterocolitis and infectious disease in infancy. In addition, probiotic supplementation commenced in the neonatal period might reduce the risk of atopic disease in later life. These data are preliminary, and a number of issues need to be resolved before general guidelines regarding the use of probiotics in the neonatal period can be given.