The newborn is first colonized by microbes at birth. The colonizing bacteria originate mainly from the mother's gut, vaginal tract and skin. The origin of the microbiota and its development depend on genetics, mode of delivery, early feeding strategies and the hygienic conditions around the child. The indigenous microbiota of an infant's gastrointestinal tract is modulated through contact and interaction with the microbiota of the parents and the infant's immediate environment. After delivery breastfeeding continues to enhance the original inoculum by specific lactic acid bacteria and bifidobacteria and bacteria from the mother's skin enabling the infant gut microbiota to be dominated by bifidobacteria. These bacteria set the basis for gut microbiotia development and modulation along with breastfeeding and the environmental exposures such as antibiotic administration. Modifying this exposure can take place by probiotic bacteria when breastfeeding is not possible. Thus, incorporating specific probiotics selected for the development of the infant's gut microbiota may form a beneficial possibility for future infant feeding purposes. Many current probiotics have documented strain-specific health-promoting effects, and most of the effects that have been demonstrated in infants and children. The target in infants is to modify the gut microbiota to resemble that of the healthy breastfed infant and to counteract deviations or aberrancies present in infants at risk of specific diseases. Thus, providing specific selected probiotics to the mother to balance the intestinal microbiota during pregnancy and to the infant after birth. As the disturbed succession during early infancy has been linked to the risk of developing infectious, inflammatory and allergic diseases later in life, it is still of great interest to further characterize both the composition and succession of microbiota during infancy. With new methodologies we have been able to identify more specific aberrancies in microbiota prior to or during different disease states.