Previously, we showed that hypoxia-inducible factor (HIF)-1alpha, HIF-2alpha, carbonic anhydrase IX (CA IX), and vascular endothelial growth factor (VEGF) were frequently coexpressed in tumor biopsies from patients of nasopharyngeal carcinoma (NPC) and were associated with poor outcome after radiotherapy. Here, we further studied hypoxic induction of HIF-1alpha, HIF-2alpha, CA IX, and VEGF in NPC cell lines, investigated hypoxia-modulated gene expression in NPC cell lines by Affymetrix GeneChip Array expression profiling, and identified pathways influenced by hypoxia and novel genes not previously recognized as hypoxia-inducible. Differentially regulated genes under hypoxia were identified genome widely and selected genes validated by RT-PCR. We found that hypoxia induced HIF-1alpha, CA IX and VEGF expression but not HIF-2alpha in NPC cells. Microarray expression analysis showed that 222 genes were commonly up-regulated and 137 genes down-regulated in hypoxic-treated CNE-2 and HONE-1 cells. Hypoxia induced broad changes of both up- and down-regulated gene expressions involved in diverse biological processes in NPC cells. Elucidation of the coordinated functions modulated by hypoxia could lead to a better understanding of the clinical significance of the hypoxic tumor phenotype.