Growth and development are determined by genetic and environmental factors since the very early embryonic life. Long-term health risks, as obesity and other non-communicable diseases (NCD), could be programmed since these early stages. Early life, characterized by plasticity, is the ideal time to intervene and to prevent the risk of suffering a NCD (window of opportunity). Optimal nutrition during the first 1,000 days, since conception to the end of the second year of life, has a determinant role for long-term health. Pregnancy, infancy and toddler periods have specific nutritional requirements. Intestinal microbiota enhances maturation and functioning of the immune system. The interactions between host and intestinal microbiota are potential factors influencing early programming of the intestinal function. Alterations in intestinal colonization are associated to a higher risk of allergic diseases in childhood. Scientific evidence supports the fact that the first 1,000 days are crucial to achieve a better long-term health and represents a strategic period to intervene under the perspective of prevention and public health.