The prevalence of allergic disorders may stem from reduced microbial exposure during childhood. Allergic disorders (rhinitis, asthma, atopic dermatitis) result from a systemic inflammatory reaction triggered by Th2-cell-mediated immune responses against ‘innocuous’ environmental antigens. Initial interpretations proposed an immune deviation of allergen-specific responses from a Th1 to a Th2 profile resulting from reduced production of interleukin-12 and interferons by natural immune cells stimulated by bacterial products. Both stereotypical and selective responses of innate host cells are invoked by different microorganisms. Early in an infection, pathogens can therefore imprint their ‘signatures’ on antigen-presenting cells and subsequent immune responses. This interaction between microorganisms and enterocytes is important for the controlled production of cytokines and chemokines. Some probiotic microorganisms can modulate the in vitro expression of pro- and anti-inflammatory cytokines in a straindependent manner, probably skew the immune response towards Th1 phenotype and play an important role in allergy prevention.