Nuclear factor-kappaB (NF-kappaB) has a central role in coordinating the expression of a wide variety of genes that control cerebral ischemia. Although there has been intense research on NF-kappaB, its mechanisms in the ischemic brain have not been clearly elucidated. We investigated the temporal profile of NF-kappaB-related genes using a complementary DNA array method in wild-type mice and human copper/zinc-superoxide dismutase transgenic (SOD 1 Tg) mice that had low-level reactive oxygen species (ROS) by scavenging superoxide. Our DNA array showed that IkappaB kinase (IKK) complex (IKKalpha, beta, and gamma) mRNA in the wild-type mice was decreased as early as 1 h after reperfusion, after 30 mins of transient focal cerebral ischemia (tFCI). In contrast, tFCI in the SOD1 Tg mice caused an increase in the IKK complex. The IKK complex protein levels were also drastically decreased at 1 h in the wild-type mice, but did not change in the SOD 1 Tg mice throughout the 7 days. Electrophoretic mobility shift assay revealed activation of NF-kappaB DNA binding after tFCI in the wild-type mice. Nuclear factor-kappaB activation occurred at the same time, as did the phosphorylation and degradation of the inhibitory protein IkappaBalpha. However, SOD 1 prevented NF-kappaB activation, and phosphorylation and degradation of IkappaBalpha after tFCI. Superoxide production and ubiquitinated protein in the SOD 1 Tg mice were also lower than in the wild-type mice after tFCI. These results suggest that ROS are implicated in transient downregulation of IKKalpha, beta, and gamma in cerebral ischemia.