Allergy, also termed type I hypersensitivity, is defined as a "disease following a response by the immune system to an otherwise innocuous antigen". The prevalence of allergies is high and escalating, with almost half the populations of North America and Europe having allergies to one or more common environmental antigens. Although rarely life-threatening allergies cause much distress and pose an important economic burden. Recent studies demonstrate the importance of the commensal bacteria of the gastrointestinal tract, termed the microbiota, in stimulating and modulating the immune system. This goes hand-in-hand with the hygiene hypothesis, proposed by Strachan in 1989. With this in mind, the use of pre- and probiotics has gained interest to prevent and treat allergies through modulation of the gut microbiota and the immune system. Probiotics, namely Lactobacilli and Bifidobacteria, are live microorganisms that can be incorporated in the diet in the form of functional foods or dietary supplements to beneficially influence the host. In recent studies, probiotic formulations demonstrated the capability to successfully modulate allergic rhinitis, atopic disorders and food-related allergies. A number of probiotic mechanisms of action are involved in controlling hypersensitivity responses, many of which are still not yet understood. Microencapsulation has gained importance as a device for the oral delivery of probiotic cells and may play an important role in the development of a successful probiotic formulation to treat and prevent allergies. Despite the promising research on probiotic biotherapeutics, further investigations are required to develop a successful therapeutic to treat and prevent allergies.