Background: Long noncoding RNAs (lncRNAs) play an important role in various biological processes involved the development and progression of lung cancer. However, their expression signature in Xuanwei lung cancer (XWLC) remains unknown. Methods: High throughput microarray assay was performed to detect lncRNA and mRNA expression profiles in five paired human XWLC and adjacent normal tissues. Bioinformatic analyses (gene ontology, pathway, and network analysis) were applied for further study of these differentially expressed mRNAs. An additional 33 paired XWLC samples were collected to verify the expression levels of 6 candidate lncRNAs using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Results: Using abundant and varied probes, about 37,000 lncRNAs and 34,000 mRNAs were assessed in our microarray. 1,484 lncRNAs and 1,997 mRNAs were differentially expressed in XWLC and adjacent normal samples (fold change >= 2.0). Using qRT-PCR validation, six candidate lncRNAs were differentially expressed in XWLC and adjacent normal tissues. The qRT-PCR results were consistent with the microarray data. Among these, FENDRR and SGOL1-AS1 were the most aberrantly expressed lncRNAs. Conclusions: This study firstly ascertained the expression profile of IncRNAs in XWLC by microarray. The results revealed that many IncRNAs were differentially expressed in XWLC and adjacent normal tissues. Further investigation of the differentially expressed IncRNAs may serve as new biomarkers for diagnosis of XWLC or novel therapeutic targets.