The aim of this study was to evaluate the effects of wheat and corn gluten on some histopathologic parameters such as villus atrophy, crypt hyperplasia, lymphocyte plasma neutrophils and immunohistochemical parameters such as trans glutaminase, gliadin and IgA in the small intestine of healthy male rats without HLA-DQ2 and HLA-DQ8 genes. In the study, 21 healthy newborn male Sprague Dawley rats were fed wheat, corn and soy with the addition of 7 rats in each group from one-day age to 60 days of age. Histopathological (villous atrophy, lymphocyte plasma neutrophil, crypt hyperplasia) and immunohistochemical (transglutaminase, gliadin, IgA) parameter analyses were performed in small intestinal tissue samples. As a result of the study, it was found that the small intestinal villus lengths of the wheat gluten group were longer than the other groups (P < .05). Cryptic hyperplasia was detected most in the soybean group and the lowest in the wheat group (P < .05). Gliadin antibody levels were found to be in the soybean group with the highest and the lowest in the wheat group (P < .05). In healthy male rats lacking HLA-DQ2 and HLA-DQ8 genes, the effect of wheat gluten on crypt hyperplasia and gliadin levels in small intestinal tissue was significantly lower than in soy and corn gluten groups, while its effect on villous atrophy, lymphocyte plasma neutrophil and transglutaminase was limited. In addition, the intestinal villus lengths of the wheat gluten group were significantly higher than those of the corn and soybean groups.