Abstract: Objective To analyze the expression of long non-coding RNA（lncRNA）in colon carcinoma. Methods We downloaded the publicly available human exon array GSE31737， which consisted of 40 paired colon carcinoma and normal adjacent tissue， from the Gene Expression Omnibus（GEO）. The probes of the human exon array were re-annotated and the probes uniquely mapping to lncRNAs at the gene level were retained. LncRNA expression profiles were generated by using Affymetrix Power Tools. The differentially expressed lncRNAs between colon carcinoma and normal adjacent tissue were analyzed by Bioconductor package LIMMA. Results We identified 136 053 probes uniquely mapping to lncRNAs at the gene level. These probes correspond to 9294 lncRNAs， covering nearly 76％ of lncRNAs in Ensembl. By analyzing GSE31737， 87 lncRNAs were differentially expressed in colon carcinoma compared with normal adjacent tissue， among which 50 were up-regulated and 37 down-regulated. Thirty-seven lncRNAs showed more than 1.5foldchange in gene expression. Conclusion LncRNA expression of colon carcinoma changes significantly in comparison with normal adjacent tissue. LncRNA may be used as a new candidate target for molecular diagnosis and gene therapy of colon carcinoma.