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The development of the intestinal microbiota occurs primarily during infancy, and a distortion could potentially contribute to a wide range of diseases. This review summarizes the current understanding of the intestinal microbiota in infants. The potential consequences of different colonization patterns on child health and possible preventive interventions are discussed.Recent studies and the use of culture-independent techniques have shown that Bifidobacterium is only a minor component of the infant gut microbiota. These techniques have also introduced the concept of a core microbiome in which metabolic function is more important than the presence of a particular bacterial species. A less diverse gut microbiota with high counts of Bacteroides, Clostridium, Enterobacteriaceae and Staphylococcus early in life has been associated with an increased risk for atopic disease. Changes in infant gut colonization were also found in relation to childhood obesity. Probiotics have no proven preventive effect on the development of asthma and an unconfirmed effect on atopic dermatitis. A prebiotic trial could show a preventive effect on the development of both atopic diseases.Molecular techniques have improved our understanding of the infant gut ecosystem. The available probiotics for prevention of atopic disease are disappointing, and the results with prebiotics need further confirmation. New studies on the relation between gut microbiota and disease should consider asthma and atopic dermatitis separately. Future trials should focus on high-risk groups, determine their long-term effect and also investigate the effect on Bacteroides and Clostridium.