The prolyl-4-hydroxylase domain enzymes PHD1, PHD2 and PHD3 function as molecular oxygen sensors, regulating hypoxia-inducible factor (HIF)-a subunit degradation by oxygen-dependent hydroxylation of two conserved prolyl residues. When oxygen supply is limited, HIF-a becomes stabilized and induces the expression of over 200 genes involved in the adaptation to hypoxia. In addition, factor inhibiting HIF (FIH) hydroxylates a C-terminal asparagine residue, triggering the transactivation activity of HIF-a. Due to their complex hydroxylation reaction mechanism, involving the substrate protein, oxygen, 2-oxoglutarate, ferrous iron and vitamin C, the PHD and FIH oxygen sensors can also be regulated by changes in transition metal concentrations, Krebs cycle intermediates, reactive oxygen species and redox conditions; suggesting that the PHDs sense more than only oxygen. Interestingly, recent data suggest the existence of HIF-unrelated targets of the oxygen-dependent protein hydroxylases, demonstrating the central role of these sensory molecules in oxygen physiology.