It is now becoming clear that the earlypostnatal environment, including nutrition,is also a vital determinant of adult health.Environmental exposures such as earlyinfant diet are believed to make an impacton the development and function of gutmicrobiota. The intestinal microbiota playsa critical role in the establishment andmaintenance of healthy immune responses.Delayed colonisation of the infant gut withcommensal bacteria or alterations in themicrobiota profile are suggested to bestrong risk factors for the development ofimmunemediated chronic disorders such asallergic and autoimmune diseases.Solid scientific arguments suggest thatimmune deviances later in life could be theconsequence of an inadequate bacterialpressure on the intestinal mucosa at theearly stage. While the role of epigeneticsin postnatal programming of the neonateremains to be demonstrated, thereappears to be a window in which infantsare vulnerable. Restoring the microbiotaprofile with a single bacteria species orprebiotic may be effective in the preventionor treatment of allergic and inflammatorydiseases, but only if this occurs during theneonatal period. The exact mechanismsof action for probiotic have yet to be fullyunderstood, but it is hypothesised that the biological function of probiotics may be aresult of epigenetic modifications that mayexplain the wide range of the observedeffectsDriving a change of colonizationduring the first weeks of life through givingprebiotic or probiotic may promote animprovement in intestinal permeability;visceral sensitivity and mast cell densityand functional nutrient administration mayrepresent a new strategy for preventingdisease later in life.