Recent studies underscore that chronic hypoxia in the tubulointerstitium is a final common pathway to progression to end-stage renal failure regardless of etiology. We used microarray analysis of rat kidneys made hypoxic by unilateral renal artery stenosis to measure transcriptomic events and clarify pathophysiological mechanisms of renal injury induced by chronic hypoxia. Many genes were upregulated in the kidney by chronic hypoxia, but we focused on metallothionein due to its antioxidative properties. Using tubular epithelial cells transfected with a reporter construct of luciferase, driven by the hypoxia-responsive elements (HRE), we found that addition of metallothionein to the culture media increased luciferase activity. This was associated with upregulation of the target genes of hypoxia-inducible factor (HIF), such as vascular endothelial growth factor and glucose transporter-1. Stimulation of the HIF-HRE pathway by metallothionein was confirmed by metallothionein overexpression. Hypoxia and exogenous metallothionein increased HIF-1alpha protein without changes in its mRNA levels, suggesting protein stabilization. Upregulation of the HIF-HRE system by metallothionein was associated with phosphorylation of ERK but not Akt. MEK inhibition and rapamycin decreased metallothionein-induced HIF activity. Our study shows that upregulation of metallothionein expression by hypoxia activates the HIF-HRE system through the ERK/mTOR pathway and may be a novel defense against hypoxia.