Increased evidence has showed that normal high density lipoprotein (HDL) could convert to dysfunctional HDL in diseases states including coronary artery disease (CAD), which regulated vascular endothelial cell function differently. Long non-coding RNAs (IncRNAs) play an extensive role in various important biological processes including endothelial cell function. However, whether IncRNAs are involved in the regulation of HDL metabolism and HDL-induced changes of vascular endothelial function remains unclear. Cultured human umbilical vein endothelial cells (HUVECs) were treated with HDL from healthy subjects and patients with CAD and hypercholesterolemia for 24 h, then the cells were collected for IncRNA-Seq and the expressions of IncRNAs, genes and mRNAs were identified. The bioinformatic analysis was used to evaluate the relationship among IncRNAs, encoding genes and miRNAs. HDL from healthy subjects and patients with CAD and hypercholesterolemia leaded to different expressions of IncRNAs, genes and mRNAs, and further analysis suggested that the differentially expressed IncRNAs played an important role in the regulation of vascular endothelial function. Thus, HDL from patients with CAD and hypercholesterolemia could cause abnormal expression of IncRNAs in vascular endothelial cells to affect vascular function. (C) 2017 Elsevier Inc. All rights reserved.