The formation of a continuous layer of normally functioning endothelium on the lumen surface of small diameter vascular grafts is considered a prerequisite of their long-term functioning without stenosis. Thus, materials supporting not only endothelialization but also the normal functioning state of endotheliocytes are demanded. In this study, we have evaluated the functional state of human umbilical vein endothelial cells (HUVEC) cultivated on the surface of autologous decellularized human umbilical vein and electrospun polyurethane-based matrices by next generation sequencing gene expression profiling. Three types of matrices produced by electrospinning from hexafluoroisopropanol solutions of pure TECOFLEX™ EG-80A polyurethane, polyurethane with gelatin and polyurethane with gelatin and bivalirudin were studied. Cells cultivated on different supports were subjected to RNA-Seq profiling on an Illumina HiSeq platform. The data demonstrated that the structure of 3D matrices and the chemical composition of the fibers have a significant effect on the gene expression profiles of HUVEC. The results suggest that protein-enriched polyurethane-based 3D matrices represent a convenient surface for obtaining a normally functioning endothelial layer.