A considerable part of the Western population suffers from some form of allergy, and the incidence is still rising with no sign of an end to this trend. Reduced exposure to microbial allergens as a result of our hygienic lifestyle has been suggested as one of the possible causes. It has also been suggested that probiotics may provide safe alternative microbial stimulation needed for the developing immune system in infants. This idea is supported by the fact that allergic infants have been observed to have an aberrant intestinal microbiota. They were shown to have more clostridia and fewer bifidobacteria and, in addition, to have an adult-like Bifidobacterium microbiota. Clinical trials have shown that the standard treatment of infants with atopic eczema, extensively hydrolyzed infant formula, can be significantly improved through the addition of Lactobacillus rhamnosus GG or Bifidobacterium lactis Bb-12. It has also been shown possible to halve the incidence of allergy in at-risk infants through administration of L. rhamnosus GG to expecting mothers and subsequently to their infants during the first half-year of life. Many mechanisms have been proposed for these beneficial effects, ranging from improved mucosal barrier function to direct influences on the immune system. However, the exact mode(s) of action are not yet known. For the future, elucidation of these mechanisms will be an important target. Another important area will be the investigation of interactions between probiotics and other food components that influence allergies. This will enable optimization of probiotic use for the allergic subject.