This review has traced the ontogeny of the human mucosal immune system, speculating that appropriate gut immune responses are essential in preventing many significant neonatal enteric diseases. Because the gastrointestinal tract serves as the portal of entry for many potential antigens, its mucosal immune function is essential in controlling antigenic responses and ensuring systemic tolerance. A thorough under standing of the development of the entire immune system is essential in defining intestinal mucosal immune function. From the protective barrier covering the enterocyte to the intraepithelial T lymphocytes, these components work together to limit antigen passage from the gut lumen to the underlying immune cells and, thus, promote normal immunity and tolerance. When abnormalities exist or when this immune barrier has not matured fully, conditions afflicting newborns, especially preterm infants, occur. Necrotizing enterocolitis, milk-protein enteropathy, and enteric bacterial infections are only three clinical examples of how aberrant gut immune-mediated defenses may have a significant role in their pathogenesis. In clinical practice, it is not only important to recognize these conditions at their onset but also to understand the basis for the underlying illness and identify newborns who are at an increased risk of acquiring them.