Exercise stimulus can be defined as endothelial wall shear stress. In the endothelial cells, the nuclear factor-kappa B (NF-κB) is an important intracellular signaling molecule by which changes in wall shear stress, sensed by mechanosensors, are transduced into the nucleus to initiate downstream eNOS gene expression. Recently, a polymorphism in the promoter region of the gene encoding a p50/p105 NF-κB subunit, NFKB1, has been identified. The NFKB1 ATTG insertion (I) / deletion (D) (NFKB1 I/D) promoter polymorphism transcriptionally regulates NFKB1 gene expression. However, the functional significance of this polymorphism has not been elucidated in endothelial cells under LSS and in endothelial function in humans. Therefore, the purpose of this study was to investigate whether the NFKB1 I/D promoter polymorphism had functional genetic properties in human umbilical vein endothelial cells (HUVECs) under physiological levels of unidirectional laminar shear stress (LSS), and further, whether the polymorphism was associated with changes in endothelial function after endurance exercise training in pre- and stage I hypertensive individuals. The major findings of the present study were that 1) a protein present in HUVECs preferentially and specifically binds to the I allele promoter compare to the D allele; 2) the I allele had significantly higher promoter activity than the D allele; and accordingly, the II homozygote cells had higher p50/p105 NFKB1 protein levels than the DD homozygote cells; 3) the II homozygote cells showed a greater increase in eNOS protein levels than the DD homozygote cells under unidirectional LSS; and 4) the I-allele carrier group had a greater reactive hyperemic forearm blood flow response, a measure of endothelial function, before exercise training; however, the NFKB1 I/D polymorphism was not significantly associated with the differential changes in endothelial function following exercise training. These results have potential clinical implications for endothelial dysfunction that are related to the development and progression of atherosclerosis and cardiovascular disease. In addition, our findings provide insight into the molecular mechanisms involved in the intracellular signaling transduction process of eNOS gene expression and function of the NFKB1 gene promoter region.