To observe the effect of the genetically modified wheat harboring GmDREB1 gene on intestinal microflora in sprague dawley (SD) rats.Methods Based on gender and weight, sixty SD rats were randomly divided into three groups:genetically modified (GM) wheat group (group A), non-GM wheat group (group B) and AIN-93 control group (group C). They were fed for 12 months. Feces samples were collected during the experiment period. Culture of fecal flora and denaturing gradient gel electrophoresis were used to investigate the bacterial profiles of the three groups. Results Compared with pre-experiment, the number of Bifidobacterium and Lactobacillus of group A and B increased significantly, which was significantly higher than those of group C (P<0.05). There were no significant differences between group A and group B in the number of the five feces flora, bands and Shannon's index (P>0.05). UPGMA cluster analysis indicated that group A and group B showed a high degree of similarity.Conclusion It was concluded that the genetically modified wheat with GmDREB1 gene had no detrimental effects on the intestinal microflora in SD rats.