Hypoxia is commonly featured during glioma growth and plays an important role in the processes underlyingtumor progression to increasing malignancy. Here we compared the gene expression profiles of rat C6 malignantglioma cells under normoxic and hypoxic conditions by cDNA microarray analysis. Compared to normoxicculture conditions, 180 genes were up-regulated and 67 genes were down-regulated under hypoxia mimicked byCoCl2 treatment. These differentially expressed genes were involved in mutiple biological functions includingdevelopment and differentiation, immune and stress response, metabolic process, and cellular physiologicalresponse. It was found that hypoxia significantly regulated genes involved in regulation of glycolysis and celldifferentiation, as well as intracellular signalling pathways related to Notch and focal adhesion, which are closelyassociated with tumor malignant growth. These results should facilitate investigation of the role of hypoxia inthe glioma development and exploration of therapeutic targets for inhibition of glioma growth.