Hypoxic preconditioning (8% O 2 , 3 h) produces tolerance 24 h after hypoxic-ischemic brain injury in neonatal rats. To better understand the ischemic tolerance mechanisms induced by hypoxia, we used oligonucleotide microarrays to examine genomic responses in neonatal rat brain following 3 h of hypoxia (8% O 2 ) and either 0, 6, 18, or 24 h of re-oxygenation. The results showed that hypoxia-inducible factor (HIF)-1-but not HIF-2-mediated gene expression may be involved in brain hypoxia-induced tolerance. Among the genes regulated by hypoxia, 12 genes were confirmed by real time reverse transcriptase-PCR as follows: VEGF, EPO, GLUT-1, adrenomedullin, propyl 4-hydroxylase ␣, MT-1, MKP-1, CELF, 12-lipoxygenase, t-PA, CAR-1, and an expressed sequence tag. Some genes, for example GLUT-1, MT-1, CELF, MKP-1, and t-PA did not show any hypoxic regulation in either astrocytes or neurons, suggesting that other cells are responsible for the up-regulation of these genes in the hypoxic brain. These genes were expressed in normal and hypoxic brain, heart, kidney, liver, and lung, with adrenomedullin, MT-1, and VEGF being prominently induced in brain by hypoxia. These results suggest that a number of endogenous molecular mechanisms may explain how hypoxic preconditioning protects against subsequent ischemia, and may provide novel therapeutic targets for treatment of cerebral ischemia.Impaired oxygen (hypoxia) or reduced blood flow (ischemia) to the brain is a major cause of morbidity and mortality in the perinatal period, often resulting in cognitive impairment, seizures, and other neurological disabilities. Although hypoxiaischemia animal models have increased our understanding of the processes leading to cell death, there are still no pharmacological treatments available to reduce cell death in ischemic neonatal brain.Interestingly, cells can be protected when a non-injurious hypoxic stress is performed several hours or days before a lethal hypoxic-ischemic stress (preconditioning). This phenomenon is called tolerance. Ischemic tolerance can be achieved in brain by several preconditioning sublethal stresses such as hypoxia (1-3), ischemia itself (4), hypothermia (5), hyperthermia (6), hyperbaric oxygenation (7), metabolic inhibitors (8), spreading depression (9), as well as cytokines (10, 11).As hypoxic preconditioning is non-invasive and reproducible, this model has been used to study the mechanisms protecting the brain against hypoxia-ischemia particularly in newborn rats (3,(12)(13)(14). In addition, hypoxic preconditioning also induces tolerance against focal transient (15) and permanent (16) cerebral ischemia in adult mice. These studies suggested that hypoxia-inducible factor-1 (HIF-1) 1 could be an important mediator of hypoxia-induced tolerance to ischemia (13,14,16). Indeed, hypoxic preconditioning induces expression of HIF-1␣ and its target genes in neonatal (14) and adult brain (16). In addition, desferrioxamine and cobalt chloride, two agents that activate HIF-1 (17), also induce tolerance against hypoxia-ischemia...