The interactions between microbes and the host have fuelled clinical research subsequent to the demonstration that a growing number of clinical conditions, ranging from allergic diseases to obesity, are linked to aberrant gut microbiota. The compositional development of the child´s gut microbiota, again, is highly sensitive to the mode of delivery and early feeding, antibiotic use and maternal immune and nutritional state during pregnancy. Importantly, pregnancy and early infancy comprise the critical stages for programming of health. The programming theory envisions health as being determined by early life events in utero and during infancy, when the key regulatory systems are sensitive to the environmental exposures. Specifically dysbiosis, an imbalance in the taxonomic composition of the gut microbiota, during these critical stages of development induces lasting alterations in the immune and metabolic phenotype. According to this hypothesis, altering the intestinal microecosystem by probiotics or prebiotics may be taken as a key target to attain prophylactic or therapeutic effects in non-communicable diseases.