In order to explore the molecular mechanism of exogenous nucleic acids improving repair of irradiation-damaged intestinal epithelium, 45 mice being irradiated by γ ray were treated with 40 μg small intestinal RNA as test group, whose small intestinal specimens were collected respectively at 6 h,12 h,24 h,4 d and 8 d after treatment; 40 mice being irradiated by γ ray were treated with physiological saline as control group, whose small intestinal specimens were collected at the same interval time. Then fragments of genes expressed in test group higher than those in control group, were obtained by using LD-PCR based on subtractive hybridization. After that, these gene fragments were cloned into T vectors,and were sequenced. Obtained sequences were searched for GenBank.90 clones associated with repair of irradiation -damaged crypt cells were obtained.In test group of 6 h, higher similar sequences mainly were as follows: mRNA for heat shock protein, Nmi mRNA, Dutt1 protein, mRNA for Na,K-ATPase gamma subunit,mRNA for surface glycoprotein,Zinc finger type transcript factor,porcine growth hormone-releasing hormone gene,Homo sapiens dual specificity phosphatase,etc. In test group of 12 h, higher similar sequences were as follows: alkaline phosphatase mRNA,alkaline phosphatase 2,glkA gene, single stranded replicative centromeric gene,Homo sapiens DMBT1 candidate tumor gene, tRNA -Met gene,mouse Ig unrearranged transcribed H-chain,thyroxine-binding globulin gene,alpha-2-plasmin inhibitor gene, etc;In test group of 24 h, higher similar sequences were as follows: anti-CEA ScFv antibody heavy chain vary region,anti-DNA antibody Ig heavy chain, mRNA for Ig kappa chain region,anti-BONT/A Hc ScFv antibody heavy chain vary region, mRNA for ScFv collagenase heavy chain vary region, AE0199 immunoglobulin heavy chain,mouse Ig gamma-chain,Ig rearranged gamma-chain mRNA,anti-NP antibody IgH,mRNA for arginine/serine kinase,dual specificity phosphatase,family mRNA telomerase-associated protein,anti-human erB-2 region,BMP-4 gene,etc; In test group of 4 d, higher similar sequences were as follows: mRNA for sodium channel,tazarotene-induced gene,betaine-GABA transporter gene,homobox protein Xgbx-2 mRNA,mRNA for stress-activated protein,FK506 binding protein,calium /calmodulin dependent gene,PEST phosphatase interactin gene,haptoglobin mRNA, etc;In test group of 8 d, higher similar sequences were as follows: Ig Mu variable region mRNA,Mus musculus Ig K chain mRNA V-region, mRNA for Hox1b protein,Mus musculus neutroactin mRNA, rat alkaline phosphatase mRNA,Human mRNA for XP-C repair complementing protein,human alpha-2-plasmin inhibitor gene,mRNA for CCAT binding factor,mouse active H-chain VJ region,etc. Eighteen were new sequences,whose function were unclear. Ninety clones were obtained to be associated with repair of damaged mice intestinal gland cells caused by γ ray and treated by small intestinal RNA.Repair of damaged intestinal gland cells treated by exogenous nucleic acids may be associated with hsp,Nmi,Dutt1,alkaline phosphatase genes and eighteen new sequences.