Long noncoding RNAs (LncRNAs) were important genes involved in a variety of biological functions. They are aberrantly expressed in many types of diseases. In this study, we described LncRNAs profiles in 4 pairs of human brain arteriovenous malformation(AVM) and the corresponding fragment of superior temporal arteries(STA) or small scalp arteries (controlled arteries, CA) and try to find LncRNAs that correlated with the human brain AVM and with clinical symptoms.4 pairs of AVM tissues and corresponding STA or scalp artery fragments (depended on the operative approach) of 4 AVM patients who were admitted in Beijing TianTan hospital were collected. Then LncRNA and mRNA expression profiling analysis was performed by Arraystar-LncRNA array. From the data, we found 1931 LncRNAs upregulated (>2 folds) and 1852 downregulated (<2 folds) in total 28,012 LncRNAs that could be detected. We also found 1577 upregulated mRNAs (>2 folds) and 1699 downregulated (<2 folds) in 21,780 mRNAs that could be detected. LncRNAs (ENST00000423394, ENST00000444114, TCONS_00013855, and ENST00000452148) were evaluated by qPCR in 14 pairs of AVM nidus and the control. This 4 LncRNAs were aberrantly expressed in AVM nidus compared with the control. LncRNA (ENST00000423394) correlated with epilepsy (R=0.34, P=.02, 95% confidence interval 0.08-0.85)We found that development of AVM may correspond with downregulation of NADPH reductase, lipoprotein lipase and Optic atrophy related proteins. It also may correspond with upregulation of Fcreceptor. The downregulation of NADPH reductase may correlate with seizures of AVM patients.