Several pathologies of the gastrointestinal tract, particularly food allergy, are due to an exaggerated and imbalanced response of the gut mucosal immune system. The intestinal microflora is an important constituent of the gut mucosal barrier against food allergens and there is increasing evidence that one important acquired factor predisposing to food allergy in infants is the gut microflora. Indeed, the balance of bifidobacteria versus Clostridia in the neonatal flora appears to determine the allergic status in infants. In earlier studies, it was shown that the higher prevalence of allergies in infants fed standard formulas, compared to breast-fed infants, correlated with lower frequencies of bifidobacteria in their faeces. Certain Lactobacillus probiotic strains can have an inhibitory impact on allergic inflammation. The mechanisms implicated are still unclear, but it seems that they can involve both proteolytic and/or immunomodulatory functions. One challenge will be to find a probiotic strain that elicits all these functions and that fulfills all safety criteria.