The gut microflora plays an important role in the development of the immune system. Its development starts after birth and the colonizing bacteria originate mainly from the mother and the environment. The most important determinants of the gut microbiotic composition are the mode of delivery and the type of infant feeding. Vaginally born and breastfed infants have their gut colonized predominantly with lactobacilli, bifidobacteria and Bacteroides fragilis, whereas the counts of Clostridium difficile and E. coli are lower. Abnormal intestinal microflora in the newborn might be a risk factor for the development of autoimmune disorders, allergy or asthma in older infants. Vaginally born and breastfed term infants seem to have the most beneficial gut microflora.