In this paper, we intended to further investigate the effects of small intestine (Ribonucleic acid, RNA), on gene expression of intestines of irradiated mice. This will provide theoretical bases for repair of γ-ray caused damage in small intestine. Twelve BALB/c mice were randomly divided into two groups, one for irradiated con- trol and the other for small intestine RNA therapy (100μg/mL, 0.4mL). Eighteen hours after γ-ray irradiation with a dose rate of 138.82 cGy/min and a total dose of 1150cGy, the mice were killed and their jejunum were taken out. Fluorescent cDNA probes labeled with Cy3 and Cy5 were prepared from RNA extracted from the intestines of the two groups. The probes of the two groups were hybridized against cDNA gene chip, the fluorescent signals were scanned with a scanner and the results were analyzed by a computer codes. Compared with the control group, 47 genes changed in gene expression profile. The expression levels of 13 genes were up-regulated distinctly, while 34 genes were down-regulated significantly. Among the 47 genes, 20 were reported with known or inferred functions, i.e. 8 up-regulated genes (arginase 1, LPS-binding protein, rpS17, IL-18, beta-1-globin,small proline-rich protein 2A, pancreatitis-associated protein,and haptoglobin gene) and 12 down-regulated genes (component 2, integral membrane protein 2, ATP synthase alpha subunit, Man- nose-6-phosphate receptor, IMP dehydrogenase, Gk-rs1, WW-domain binding protein1, ubiquitin fusion degrada- tion1, α1-actin, natural killer cell protein group 2, UDP-glucose dehydrogenase, and EMK2 gene). The other 27 were reported with unknown functions. In conclusions, small intestine RNA could change specific expressions of some genes in mouse small intes- tines and most of these genes were down-regulated ones.