Context: Activation of the hypoxia inducible transcription factors HIF-1 and HIF-2 and a HIF-independent defect in developmental apoptosis have been implicated in the pathogenesis of phaeochromocytoma(PCC) associated with VHL, SDHB and SDHD mutations. Objective: To compare protein (HIF-1, EPAS1, SDHB, JunB, CCND1, CD34, CLU) and gene (VEGF, BNIP3) expression patterns in VHL and SDHB/D associated tumors. Results: Overexpression of HIF-2 was relatively more common in VHL than SDHB/D PCC (12/13 vs. 14/20, P = 0.02), whereas nuclear HIF-1 staining was relatively more frequent in SDHB/D PCC (19/20 vs. 13/16, P = 0.04). In addition CCND1 and VEGF expression (HIF-2 target genes) was significantly higher in VHL -than in SDHB/D PCCs. These findings suggest that VHL inactivation leads to preferential HIF-2 activation and CCND1 expression as described previously in VHL-defective renal cell carcinoma (RCC) cell lines but not in other cell types. These similarities between the downstream consequences of VHL inactivation and HIF dysregulation in RCC and PCC may explain how inactivation of the ubiquitously expressed VHL protein results in susceptibility to specific tumor types. Both VHL and SDHB/D PCC demonstrated reduced CLU and SDHB expression. SDHB PCC are associated with a high risk of malignancy and expression of (proapototic) BNIP3 was significantly lower in SDHB than VHL PCC. Conclusion: Although inactivation of VHL and SDHB/D may disrupt similar HIF-dependent and HIF-independent signaling pathways, their effects on target gene expression are not identical and this may explain the observed clinical differences in PCC and associated tumors seen with germline VHL and SDHB/D mutations.