Probiotic bacteria as modulators of the immune response have been intensively studied in reducing the risk of immune-mediated diseases, including atopic diseases. Results from in vitro studies demonstrated that probiotics may modify the polarization of immune cells, supporting potential therapeutic effects in atopic diseases. Several clinical studies have been designed to explore the effective role of probiotics in the modulation of allergic diseases. The results of these studies, although promising, are not conclusive yet and are considered insufficient to recommend probiotics as a part of standard therapy in any allergic conditions. In vivo studies on animal models can provide useful information on the immunologic mechanisms responsible for the potential antiallergic effects of probiotic bacteria. The immunomodulatory activity of the probiotic mixture VSL#3 has been studied in the mouse models of allergic sensitization and anaphylaxis developed in our laboratory with inhalant and food allergens, according to a prophylactic setting by the intranasal route (inhalant allergy model) or a therapeutic setting by the oral route (food allergy model). Intranasally delivered probiotic bacteria prevented the development of Parietaria major allergen-specific response, by down-regulating T helper cell 2 responses at the local and systemic level. Oral therapeutic treatment was able to reduce both systemic and local anaphylactic symptoms induced by oral challenge with the sensitizing allergen Shrimp Tropomyosin. The induction of protective immune responses at the sites of allergen exposure linked to counterregulatory local and systemic immune responses by mucosal delivery of probiotic bacteria mixtures might become an effective strategy in the prevention and therapy of allergic diseases.