NF-kappaB signaling pathway has been known to play a major role in the pathological process of atherogenesis. Unlike high shear stress, in which the NF-kappaB activity is transient, our earlier studies have demonstrated a persistent activation of NF-kappaB in response to low shear stress in human aortic endothelial cells. These findings partially explained why low shear regions that exist at bifurcations of arteries are prone to atherosclerosis, unlike the relatively atheroprotective high shear regions. In the present study, we further investigated 1) the role of NF-kappaB signaling kinases (IKKalpha and beta) that may be responsible for the sustained activation of NF-kappaB in low shear stress and 2) the regulation of these kinases by reactive oxygen species (ROS). Our results demonstrate that not only is a significant proportion of low shear-induced-kinase activity is contributed by IKKbeta, but it is also persistently induced for a prolonged time frame. The IKK activity (both alpha and beta) is blocked by apocynin (400 microM), a specific NADPH oxidase inhibitor, and diphenyleneiodonium chloride (DPI; 10 microM), an inhibitor of flavin-containing oxidases like NADPH oxidases. Determination of ROS also demonstrated an increased generation in low shear stress that could be blocked by DPI. These results suggest that the source of ROS generation in endothelial cells in response to low shear stress is NADPH oxidase. The DPI-inhibitable component of ROS is the primary regulator of specific upstream kinases that determine the persistent NF-kappaB activation selectively in low shear-induced endothelial cells.