Breastfeeding confers the infant short- and long-term health benefits and significantly modulates the developing infant gut microbiome. A specific human milk microbiome has relatively recently been discovered, but its origin remains poorly understood. Data from experimental and clinical studies suggest that the bacteria in milk may originate in the maternal gut and be transported via a specific enteromammary pathway, the details of which have not been elucidated yet. The milk microbiome is affected by the maternal metabolic state, antibiotic use, as well as the mode of delivery. We are only in the initial stages of understanding the biological function of the milk microbiome and its potential contribution to infant gut colonization. Several clinical studies indicate, however, that despite considerable differences in the overall composition of the milk and infant gut microbiomes, specific bacteria are detectable both in human milk and infant feces, and that the bacteria in milk are a source of microbes colonizing the neonatal gut. If the microbes in human milk are discovered to contribute to the beneficial effects of breastfeeding, modulating or mimicking the milk microbiome may provide a novel means of improving child health.