The gastrointestinal microbiota plays an important role in maintaining host health by preventing the colonization of pathogens, fermenting dietary compounds, and maintaining normal mucosal immunity. Particularly in early life, the composition of the microbiota profoundly influences the development and maturation of the gastrointestinal tract (GIT) mucosa, which may affect health in later life. Therefore, strategies to manipulate the microbiota during infancy may prevent the development of some diseases later in adult life. Earlier research suggested that term fetuses are sterile and that the initial bacterial colonization of the newborn GIT occurs only after the baby transits through the birth canal. However, recent studies have demonstrated that the colonization and/or contact of the fetus with the maternal GIT microbiota may start in utero. After vaginal birth, the colonization of the neonate GIT continues through contact with maternal feces and vaginal bacteria, leading to a relatively simple microbial community that is influenced by feeding type (breast vs. formula feeding). Maternal GIT microbiota, vaginal microbiota, and breast milk composition are influenced by maternal diet. Alterations of the maternal GIT microbiota composition via supplementation with probiotics and prebiotics have been shown; however, transfer of these benefits to the offspring remains to be demonstrated. This review focuses on the influence of maternal GIT microbiota during the pre- and postpartum periods on the colonization of the infant GIT. In particular, it examines the manipulation of the maternal GIT microbiota composition through the use of probiotics and/or prebiotics and subsequent consequences for the health of the offspring.