Epigenetic modifications are among the most important mechanisms through which environmental factors can influence early cell differentiation and create new phenotypic traits during pregnancy and early childhood without altering the deoxyribonucleic acid sequence. Many prenatal and postpartum factors, such as maternal and neonatal nutrition, pollutant exposure, and microbiota composition, contribute to the establishment of epigenetic modifications that affect not only an individual’s adaptation to the environment but also lifelong health and disease by altering signaling pathways and immune responses. Postpartum intestinal colonization, determined by the maternal microbiota and neonatal nutrition, leads to specific epigenetic modifications that may affect intestinal mucosal properties and their protective role in the development of inflammatory diseases later in life. In mammals, there are two main time periods where the epigenome is erased and re-established, namely gametogenesis and fetal development. Fetal development has three developmental stages, the period before implantation, the period of embryonic development, and the postpartum transition. Therefore, even woman's diet before they want to conceive is a big factor influencing a child’s development. Also, a pregnant woman at all stages of fetal development and a breastfeeding mother should be very careful in their diet, as insufficiently varied foods or foods rich in individual nutrients lead to changes in methylation motives that affect the development of the disease. The role of maternal nutrition during pregnancy and after childbirth, the child's diet and its microbiota and other nutritional factors strongly influence the determination of epigenetic modifications and their short- and long-term effects on the health and development of the child.