The increase in the prevalence of allergic diseases in children has been attributed to an unbalanced immune response probably due to environmental factors. The immunoregulatory properties of probiotic bacteria could balance the disequilibrium in the immune response causing the allergic response. The aim of this study was to evaluate the immunological effects of the consumption of a dairy product containing two probiotic strains in children suffering from allergy. A double-blinded, randomized, control comparative study was performed with 44 allergic children. Children were randomly distributed in two groups, a control Yogurt and a Probiotic group. Both groups daily consumed 200 ml of a dairy fermented product for 3 months. The Yogurt group consumed a conventional yogurt, whereas the Probiotic group consumed a similar dairy product where Lactobacillus bulgaricus was substituted by a mixture of Lactobacillus gasseri CECT5714 and Lactobacillus coryniformis CECT5711 (at least 106 cfu/g each strain). Intestinal and immunological parameters were measured in fecal and blood samples. The consumption of the probiotic product induced a significant decrease in the level of IgE in plasma (p = 0.03) and an increase in CD4+/CD25+ T regulatory cells (p = 0.01). The decrease in IgE was accompanied by a significant increase in mucosal IgA (p = 0.01). However, changes in other effector cells potentially involved in allergic reactions such as eosinophiles, basophiles or other IgE+ cells were not detected. The consumption of the probiotic product also induced significant changes in innate response as a significant increase in natural killer cells was detected (p = 0.03). The daily consumption of a probiotic product containing L. gasseri CECT5714 and L. coryniformis CECT5711 for 3 months induces, in allergic children, beneficial effects on immune parameters involved in the allergic response such as a reduction of IgE in plasma and an increase in regulatory T cells. The probiotic product also enhanced innate and specific immune parameters that may improve the general health status of children.