The intestinal microbiota plays an important role in the development of post-natal gastrointestinal functions of the host. Recent advances in our capability to identify microbes and their function offer exciting opportunities to evaluate the complex cross talk between microbiota, intestinal barrier, immune system and the gut-brain axis. This review summarizes these interactions in the early colonization of gastrointestinal tract with a major focus on the role of intestinal microbiota in the pathogenesis of feeding intolerance in preterm newborn. The potential benefit of early probiotic supplementation opens new perspectives in case of altered intestinal colonization at birth as preventive and therapeutic agents.