Hypoxia-inducible factor (HIF), consisting of a labile ␣ subunit and a stable  subunit, is a master regulator of hypoxia-responsive mRNAs. HIF␣ undergoes oxygen-dependent prolyl hydroxylation, which marks it for polyubiquitination by a complex containing the von Hippel-Lindau protein (pVHL). Among the three Phd family members, Phd2 appears to be the primary HIF prolyl hydroxylase. Phd3 is induced by HIF and, based on findings from in vitro studies, may participate in a HIF-regulatory feedback loop. Here, we report that Phd3 loss exacerbates the HIF activation, hepatic steatosis, dilated cardiomyopathy, and premature mortality observed in mice lacking Phd2 alone and produces a closer phenocopy of the changes seen in mice lacking pVHL than the loss of Phd2 alone. Importantly, the degree to which Phd3 can compensate for Phd2 loss and the degree to which the combined loss of Phd2 and Phd3 resembles pVHL loss appear to differ for different HIF-responsive genes and in different tissues. These findings highlight that the responses of different HIF target genes to changes in prolyl hydroxylase activity differ, quantitatively and qualitatively, in vivo and have implications for the development of paralog-specific prolyl hydroxylase inhibitors as therapeutic agents.Many human diseases, including anemia, myocardial infarction, and stroke, are closely linked to tissue hypoxia. The transcriptional response to hypoxia in metazoans is mediated primarily by the heterodimeric transcriptional factor hypoxiainducible factor (HIF), which consists of an ␣ subunit (HIF␣) and a  subunit (HIF, also called the aryl hydrocarbon receptor nuclear translocator) (21). Under hypoxic conditions, HIF␣ accumulates, dimerizes with HIF, translocates to the nucleus, and transcriptionally activates genes containing hypoxia response elements. Many of these genes regulate processes, such as erythropoiesis, angiogenesis, and energy metabolism, that affect oxygen delivery or oxygen consumption and thereby affect survival in a low-oxygen environment (47).There are three HIF␣ family members in humans, called HIF1␣, HIF2␣, and HIF3␣. Both HIF1␣ (the canonical HIF␣ family member) and HIF2␣ contain two transactivation domains, the N-terminal transactivation domain (NTAD) and the C-terminal transactivation domain (CTAD), and can activate transcription when bound to DNA. Whether HIF3␣ activates transcription is less certain. Multiple HIF3␣ splice variants have been identified, at least some of which are dominantinterfering with respect to HIF␣ activity (31, 32).The mechanism that couples the accumulation of HIF␣ to oxygen availability has recently come into view. When oxygen is plentiful, HIF␣ becomes hydroxylated at one (or both) of two conserved prolyl residues (21). HIF␣ hydroxylated at one prolyl residue is recognized by a ubiquitin ligase complex that contains the von Hippel-Lindau tumor suppressor protein (pVHL), polyubiquitinated, and degraded by the proteasome. Caenorhabditis elegans and Drosophila species contain a single prolyl hydroxylase, calle...