The infant microbiota colonization process runs in parallel with immune system maturation, affecting intestinal physiology and regulation. Accumulating evidence suggests that microbial exposition begins before birth (in utero) and continues after birth. It is shaped by mode of delivery, and breastfeeding practices are the most important factors. The maternal microbiota is the main source of microorganisms for the infant gut, and breast milk constitutes the most important source of post-natal microbes. From birth onwards, infant microbial diversity increases and converges towards an adult-like microbiota at 3–5 years of life. Imbalances in this microbial colonization are considered strong risk factors for the development of non-communicable diseases. According to available data, an adequate nutritional and microbial environment in early life is key in microbiological, immunological and metabolic programming of infant health.