In polycystic kidney disease (PKD), erythropoietin (EPO) production and interstitial vascularization are increased compared with other kidney diseases. EPO and several angiogenic factors are controlled by hypoxia-inducible transcription factors (HIFs), which are composed of a constitutive β-subunit and two alternative α-subunits (HIF-1α, HIF-2α). We hypothesized that cyst expansion may result in pericystic hypoxia and consecutive up-regulation of HIF and thus examined the expression of HIF-α and HIF target genes in human PKD and in a rodent PKD model. HIF-1α and HIF-2α were found to be up-regulated in cyst epithelium and cells of cyst walls, respectively. The distinct expression pattern of the HIF-α isoforms closely resembles the respective pattern in normal kidneys under systemic hypoxia. Pimonidazole staining, a marker for tissue hypoxia, confirmed the existence of regional hypoxia in polycystic kidneys. Immunohistochemistry for selected target genes implicated a role for HIF-1α in vascular endothelial growth factor and Glut-1 activation and HIF-2α in endoglin and EPO stimulation. Polycystin-deficient cells showed physiological, oxygen-dependent HIF-α modulation, excluding a direct influence of polycystin deficiency on HIF-α regulation. In conclusion, HIF accumulation in human and rat PKD seems to be responsible for increased EPO production and pericystic hypervascularity and may have an impact on progression of PKD.