ABSTRACT: Beginning with the observation that birth weight correlates with increased risk of cardiovascular disease, the concept of neonatal programming, that the environmental influence on fetal and neonatal development results in modification of the risk profile for adult disease, has begun to emerge as an important component to understanding the origin of chronic diseases of many different organ systems. Until recently, the gastrointestinal system has not been considered. Our understanding of the pathogenesis of many intestinal inflammatory disorders is still incomplete; however, a brief review of what is known reveals several opportunities for the early intraluminal environment to affect the development of the intestinal immune system. Early clinical observations such as the increased risk of celiac disease observed in those born by cesarean section and the protective effect of breast-feeding against inflammatory bowel disease and celiac disease support the role of neonatal programming in the development of chronic inflammatory gastrointestinal disease. Additional, more robust clinical studies are needed to confirm this role. Furthermore, examination of the possible mechanisms of immune phenotype modification is necessary.