The interplay between both heredity and environmental factors seems to affect every stage of development from conception to the early postnatal period with potential long-term effects on child and adult health. During pregnancy, immune and metabolic functions of the fetus are dependent on the mother; moreover, the refinement of these functions seems to commence inside the uterus and to be diet sensitive. The microbiota inhabiting the intestinal tract develop an array of physiologic roles within the human body, which influences both metabolic and immune functions, particularly during early neonatal life and possibly even in utero. Transmission of bacteria from the mother to the neonate through direct contact with maternal microbiota during birth and through breast milk during lactation also seems to influence the infant's gut colonization, with potential health consequences. In this context, intentional modulation of microbiota composition through the use of probiotics during the perinatal and early postnatal period has been proposed as a possible dietary strategy to reduce risk of disease. Herein, studies are reviewed on the composition of the intestinal microbiota during pregnancy and clinical trials evaluating the effects of perinatal administration of probiotics on different clinical outcomes.