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Hypoxia-inducible genes have been linked to the aggressive phenotype of cancer. However, nearly all work on hypoxia-regulated genes has been conducted in vitro on cell lines. Here the hypoxia transcriptome in primary human bladder cancer was investigated using cIDNA microarrays to compare genes induced by hypoxia in vitro in bladder cancer cell line EJ28 with genes upregulated on an in vivo array of 39 bladder tumours (27 Ta/T1 12 T2-T4). mRNA array fold-changes were correlated with carbonic anhydrase IX (CA IX) staining and necrosis of tumours as surrogate markers of hypoxia. Of 6000 genes 32 were repeatedly hypoxia-inducible in vitro more than 2-fold, five of which were novel, including lactate transporter SLC16A3 and RNAse 4. Eight of 32 hypoxia-inducible genes in vitro were also upregulated on the vivo array. Vascular endothelial growth factor (VEGF) mRNA was upregulated 2-fold by hypoxia and 2 to 18-fold in 31/39 tumours. Also up regulated on both arrays was GLUT 1 mRNA, and fold changes on the in vivo genearray significantly correlated with CA IX staining of tumours (p=0.008). However Insulin-like growth factor binding protein 3 (IGFBP-3) mRNA was the most strongly differentially expressed gene in both arrays and its upregulation was confirmed in the urine of bladder cancer patients (n=157, p<0.01) and in cell line supernatants. Angiogenin was also upregulated in urine of bladder cancer patients. Selected genes upregulated by hypoxia (HIF la, HIF 2a, CA IX and NIP3) were studied by immunohistochemistry for their prognostic significance and association with necrosis in 98 cystectomy specimens. Normal human urothelial cells were also grown in culture and a hypoxia genearray profile compared with EJ28, peripheral blood monocytes and T-cells. This thesis studies the prevalence of hypoxia and necrosis in bladder cancer, its relationship with prognosis, genes associated with the hypoxic phenotype and hypoxia related molecular pathways.