The normal human microflora is a complex ecosystem that is in part dependent on enteric nutrients for establishing colonization. The gut microbiota are important to the host with regard to metabolic functions and resistance to bacterial infections. At birth, bacterial colonization of a previously germ-free human gut begins. Diet and environmental conditions can influence this ecosystem. A breast-fed, full-term infant has a preferred intestine microbiota in which bifidobacteria predominate over potentially harmful bacteria, whereas in formula-fed infants, coliforms, enterococci, and bacteroides predominate. The pattern of bacterial colonization in the premature neonatal gut is different from that in the healthy, full-term infant gut. Those infants requiring intensive care acquire intestinal organisms slowly, and the establishment of bifidobacterial flora is retarded. A delayed bacterial colonization of the gut with a limited number of bacterial species tends to be virulent. Bacterial overgrowth is one of the major factors that promote bacterial translocation. The aberrant colonization of the premature infant may contribute to the development of necrotizing enterocolitis. Breast-feeding protects infants against infection. Oligo-saccharides and glycoconjugates, natural components in human milk, may prevent intestinal attachment of enteropathogens by acting as receptor homologues. Probiotics and prebiotics modulate the composition of the human intestinal microflora to the benefit of the host. These beneficial effects may result in the suppression of harmful microorganisms, the stimulation of bifidobacterial growth, or both. In the future, control and manipulation of the bacterial colonization in the neonatal gut may be a new approach to the prevention and treatment of intestinal infectious diseases of various etiologies.