Abstract: Objective To explore specific long non-coding RNA(lncRNA) related to the occurrence and development of nasopharyngeal carcinoma(NPC) by analyzing lncRNA expression profile in NPC and chronic nasopharyngitis(CNP) tissues. Methods To screen the differentially expressed lncRNA and mRNA, lncRNA and mRNA expression profiles between NPC and CNP tissues were analyzed by microarrays. Bioinformatic analyses, such as clustering analysis, gene ontology analysis and pathway analysis, were used for further research. Results A total of 856 lncRNAs were differentially expressed with more than two-fold change (P<0.05), 425 were up-regulated and 431 were down-regulated in NPC tissues. A total of 767 mRNAs were differentially expressed, 426 were up-regulated and 341 were down-regulated. These lncRNAs were divided by clustering analysis method into three sub-groups, enhancer-like lncRNA, HOX cluster and lincRNA. GO analysis was performed to clarify the mRNAs into three kinds, biological process, cellular component and molecular function.Pathway analysis indicated that 28 signaling pathways corresponded to up-regulated and down-regulated mRNA. The enrichment score of up-regulated mRNAs participated in the pathway of cytokine-cytokine receptor interaction was the highest. Conclusion lncRNAs are significantly differentially expressed between NPC and CNP tissues. Specific lncRNA may play a key role in the occurrence and development of NPC.