This review considers the hypothesis that nutrition during infancy affects developmental epigenetics in the gut, causing metabolic imprinting of gastrointestinal (GI) structure and function. Fundamentals of epigenetic gene regulation are reviewed, with an emphasis on the epigenetic mechanism of DNA methylation. Recent data indicate that transient nutritional and other stimuli during critical periods of prenatal and early postnatal development can affect the establishment or developmental maturation of gene-specific DNA methylation, thereby inducing permanent changes in gene expression. Although epigenetic processes are clearly involved in postnatal mammalian GI development, we currently know very little about these mechanisms. Data indicating that epigenetic gene regulation plays an important role in GI development and pathology are reviewed, and suggestions for future research in this area are offered.