The ternary complex factor Net/Elk3 is downregulated in hypoxia and participates in the induction by hypoxia of several genes, including c-fos, vascular endothelial growth factor and egr-1. However, the global role of Net in hypoxia remains to be elucidated. We have identified, in a large-scale analysis of RNA expression using microarrays, more than 370 genes that are regulated by Net in hypoxia. In order to gain insights into the role of Net in hypoxia, we have analysed in parallel the genes regulated by HIF-1α, the classical factor involved in the response to hypoxia. We identified about 190 genes that are regulated by HIF-1α in hypoxia. Surprisingly, when we compare the genes induced by hypoxia that require either Net or HIF-1α, the majority are the same (75%), suggesting that the functions of both factors are closely linked. Interestingly, in hypoxia, Net regulates the expression of several genes known to control HIF-1α stability, including PHD2, PHD3 and Siah2, suggesting that Net regulates the stability of HIF-1α. We found that inhibition of Net by RNAi leads to decreased HIF-1α expression at the protein level in hypoxia. These results indicate that Net participates in the transcriptional response to hypoxia by regulation of HIF-1α protein stability.