Bacterial colonization of the neonatal gastrointestinal tract begins during birth when the neonate comes into contact with the maternal cervical and vaginal flora. In infants delivered by Caesarean section, bacteria colonizing the neonate gastrointestinal tract are provided by the environment. The first bacteria encountered in the majority of healthy infants, are facultative anaerobes, which remain predominant during the first 2 weeks of life. Among them, Staphylococcus, Enterobacteriaceae and Streptococcus were the genera most commonly isolated from the newborn faecal flora at birth. Facultative anaerobic bacteria are followed closely by Bifidobacterium sp. Clostridium perfringens is present within 2 days with an increase incidence in newborns delivered by a Caesarean section. Clostridium perfringens seems to be the precursor for installation of other anaerobic putrefactive bacteria, as Bacteroides and other Clostridium sp. The impact of Caesarean section and the period and quality of hospitalization are mainly implicated in changes of the normal newborn flora. Feeding seems to modulate the colonization pattern. In humans, breast milk plays a role in passive immunization of the neonatal intestine, and contains factors that promote the growth of Bifidobacterium bifidum in the intestinal flora. Formula feeding seems to promote implantation and persistence of Clostridium perfringens, and clearly enhances intestinal colonization of C. difficile in newborns.