Most clear cell renal cell carcinomas (ccRCCs) have inactivation of the von Hippel-Lindau tumor suppressor protein (pVHL), resulting in the accumulation of hypoxia-inducible factor ␣-subunits (HIF-␣) and their downstream targets. HIF-2␣expression is particularly high in ccRCC and is associated with increased ccRCC growth and aggressiveness. In the canonical HIF signaling pathway, HIF-prolyl hydroxylase 3 (PHD3) suppresses HIF-2␣ protein by post-translational hydroxylation under sufficient oxygen availability. Here, using immunoblotting and immunofluorescence staining, qRT-PCR, and siRNA-mediated gene silencing, we show that unlike in the canonical pathway, PHD3 silencing in ccRCC cells leads to down-regulation of HIF-2␣ protein and mRNA. Depletion of other PHD family members had no effect on HIF-2␣ expression, and PHD3 knockdown in non-RCC cells resulted in the expected increase in HIF-2␣ protein expression. Accordingly, PHD3 knockdown decreased HIF-2␣ target gene expression in ccRCC cells and expression was restored upon forced HIF-2␣ expression. The effect of PHD3 depletion was pinpointed to HIF2A mRNA stability. In line with these in vitro results, a strong positive correlation of PHD3 and HIF2A mRNA expression in ccRCC tumors was detected. Our results suggest that in contrast to the known negative regulation of HIF-2␣ in most cell types, high PHD3 expression in ccRCC cells maintains elevated HIF-2␣ expression and that of its target genes, which may enhance kidney cancer aggressiveness. This work was supported by Cancer Foundation Finland (to P.M. and P.M.J.), The Sigrid Juselius Foundation (to P.M.J.), Turku University Hospital (EVO1303) (to P.M., H.H. and P.M.J.), Helsinki University Hospital (to P.M. and P.M.J.), The University of Turku Graduate School (to P.M.), and Finnish Cultural Foundation Varsinais-Suomi Regional fund (to P.M.).