Allergy is a hypersensitivity reaction mediated by specific antibody-mediated or cell-mediated immunologic mechanisms and clinically manifested as atopic eczema, allergic rhinoconjunctivitis, or asthma. During the recent decades there has been an increase in allergy prevalence, which is attributed to changes in environmental factors. The so-called "hygiene hypothesis" suggests that a lack of exposure to microbial stimulus early in childhood is a major factor involved in this trend. This provides a rationale for using probiotics to modify the gut microbiota and thereby shaping the immune response of the host, especially in infancy. Most success has been obtained in primary prevention of atopic eczema. A limited number of studies also provided evidence for a beneficial effect of different probiotics in the management of allergic diseases (atopic eczema, allergic rhinitis). However, choice of probiotic strains as well as timing of the intervention are important variables. The exact in vivo mechanism of probiotics in shaping the immune response still needs to be determined. Future studies should use uniform criteria for diagnosis and symptom scoring of atopic diseases and may identify the genes predisposing to allergic disease. There is encouraging evidence that specific probiotics can become valuable tools in the prevention and management of allergic diseases.