Objective In order to provide the basis for establishment of food allergy models, we compared the differences of sensitivity and alterations of intestinal flora of food allergy models in two strains of mice. Methods Forty 4-5-week old female BALB/c and Kunmimg mice were divided into control group (n=10) and food allergy goup (n=30), respectively. Ovalbumin (OVA) was injected to the mice to establish food allergy models. Serum OVA-specific IgE of the mice was assayed by ELISA. The jejunum tissue was examined by pathology with HE staining. The changes of fecal flora were detected by denaturing gradient gel electrophoresis (DGGE). Results (1)Among the sensitized 60 mice, OVA-sIgE levels were significantly increased in 27/30 BALB/c mice and 21/30 KM mice compared with those of control groups(P<0.001). Moreover, there were more evident inflammatory cell infiltration, epithelial cell shedding and cytolysis in the jejunal villi of BALB/c mice than those of KM mice. (2) After food allergy modeling, there were significant changes of intestinal flora in the BALB/c mice (P<0.001), while only significant change of evenness was found in the KM mice (P<0.05). (3)There were changes of abundance, Shannon index and evenness of intestinal flora in the model groups of BALB/c and KM mice. Conclusions BALB/c mice are more sensitive to OVA allergy than KM mice. The composition of intestinal flora is different among different strains of mice. The changes of intestinal flora after OVA challenge in BALB/c mice are more obvious than those in KM mice.