The establishment of the intestinal microbiota commences at birth and new bacteria establish in succession during the first years of life until an adult-type highly complex microbiota has been achieved. The first bacteria to establish in the neonatal gut are usually aerobic or facultatively anaerobic bacteria, like enterobacteria, enterococci and staphylococci. During their growth they consume oxygen and change the intestinal milieu making it suitable for the proliferation of anaerobic bacteria. Bifidobacterium, Clostridium and Bacteroides are among the first anaerobes establishing in the microbiota. As more oxygen-sensitive species establish and the complexity of the microbiota increases, the population sizes of aerobic and facultative bacteria decline. This phenomenon is thought to result from oxygen depletion, substrate competition and the accumulation of toxic metabolites. A wide range of factors influence the intestinal microbiota and its establishment, including delivery and feeding mode, antibiotic treatment, and contacts with parents, siblings, and hospital staff. Differences in colonization pattern can be observed between vaginally and sectiodelivered infants, and between infants in industrialized and developing countries, reflecting the importance of maternal microbiota and the environment as sources of colonizing bacteria. This article describes the intestinal colonization pattern in human infants, and reviews factors affecting this process.