The early-life gut microbiome is important for the development of immune competence in newborn infants. Mode of delivery, perinatal antibiotic use and diet are most influential to this end. Breastfeeding is associated with lower risk of gastrointestinal and respiratory infections, and possibly lower risk of diabetes and obesity, while the effect on allergies is not so clear. This suggests that breast milk-specific components may contribute. Among them are the non-digestible human milk oligosaccharides (HMOs), the third largest solid breast milk component that varies primarily due to the maternal genotype for the Secretor and Lewis genes and stage of lactation. Other milk oligosaccharides are also relevant here.