Microbiological risk in the first part of life is endowed with peculiar features when compared to the same risk in adulthood. The purpose of this review is to highlight these age-related traits. While pathogens harmful for neonates and infants have been reviewed, less attention has been paid to the role played by the infant gut as battle field between pathogens and protecting bacteria or between pathogens and the immune system. Immediately after birth a race for colonizing the gut begins; the main tool for neonates to select good bacteria is represented by mother's milk. Quite surprisingly, this milk carries potentially harmful bacteria, but antibodies, oligosaccharides and the whole breast milk composition provide a powerful selective tool. Nevertheless this selective action is deeply influenced by the type and/or time (i.e. premature) of delivery or in premature subjects; recent data also show that breast milk could have a different potential in selecting bacterial species. The hygienic conditions of parents and, more generally, of the surrounding environment play a role in the selection of the intestinal biota of infants. It is then possible to group neonates according to the composition of the microbiota. Results of ecological studies suggest that neonates with a different microbiota could have a different microbiological risk.