Nutrition plays a major role in the modulation of the evolving human gut influencing all the main components of the intestinal ecosystem. The regulatory role of nutrition is particularly crucial in the early postnatal period but it continues also in subsequent ages when the development of the gastrointestinal tract is completed. Recent data support the hypothesis that nutrition can affect some inherited disorders of gastrointestinal tract. These "epigenetic" mechanisms are involved in the development of intestinal enzymes, hormones, transporters, and immunity. This is an expanding research area related to the possible nutritional intervention in selected clinical condition. This paper is focused on the main components and mechanisms of action of the nutritional modulation on intestinal development.