The probiotic activity of Lactobacillus murinus against food allergy was investigated. Oral administration with L. murinus restored the deteriorated profile of enteric flora in mice with food allergy and attenuated allergic responses, including allergen-induced diarrhoea, mast cell activation, and serum IgE production. The production of IFN-γ and IL-4 by splenocytes was enhanced and suppressed, respectively, by L. murinus administration. Concordantly, a decreased expression of IL-4 and GATA3 and an increased expression of IFN-γ and T-bet were observed in the duodenum. Moreover, L. murinus enhanced IL-12 production and suppressed OX40 ligand expression by intestinal CD11c+ cells. Direct exposure to heat-killed L. murinus enhanced IFN-γ secretion by mesenteric lymph node cells. These findings demonstrate that L. murinus possesses anti-allergic activities via modulating enteric flora, intestinal CD11c+ cell functionality and the Th1/Th2 immunobalance, and suggest that L. murinus may be employed as a functional probiotic against food allergy.