Zinc finger protein 496 belongs to the most abundant and functionally diverse family of C2H2 type transcription factors. Recently, ZNF496 was reported as both transcription repressor and activator functioning either by directly binding to DNA or by recruiting a co-factor. The aim of this study was to identify genes and biological processes regulated by ZNF496 in human umbilical vein endothelial cells (HUVEC). Total RNA extracted from HUVEC transfected with either ZNF496 siRNA (knockdown) or negative control siRNA (control) were hybridized on two- color 4x44K Whole Human Genome Oligo Microarray Chip. Microarray data was analyzed using GeneSpringGX software and unpaired t-test together with Westfall-Young Permutative multiple testing was applied for the statistical test of the microarray data. A total of 1339 (3.29%) differentially expressed genes were identified(fold change ≥ |2|, p- value <0.05) in the knockdown compared to the control RNA samples. Of which, 635 (47.42%) genes were up-regulated and 704 (52.58%) were down-regulated. Most of the genes were involved in receptor binding molecular function in the cell communication and signaling biological processes on the membrane part of HUVEC cells (p<0.05). ID, NOTCH, Wnt, IL-6, MeSH atherosclerosis and TGFBR pathways were among the significantly identified pathways (p< 0.05, FDR<0.05). In conclusion, knockdown of ZNF496 affected expression of several genes and associated pathways and biological processes. This suggests the importance of ZNF496 in the regulation of important aspects of HUVEC cell physiology and provides a vital clue for future studies.