Abstract The aryl hydrocarbon receptor nuclear translocator (Arnt) and hypoxia-inducible factor (HIF)-1α mediate cellular responses to hypoxia. We investigated the ability of hypoxia to regulate Arnt and HIF-1α mRNA in the heart in vivo. We cloned avian Arnt, developed an in vivo model of chronic cardiac hypoxia, and measured expression of cardiac Arnt and HIF-1α mRNA by quantitative RT-PCR. Chronic hypoxic exposure (24 h to 15% O2) of day 9 chick embryos resulted in a 30-fold increase in covalent binding of 3H-misonidazole, a hypoxic tissue marker, to cardiac tissue, and a 2-fold induction of cardiac inducible nitric oxide synthase mRNA, compared to normoxic controls. In this same model, cardiac Arnt mRNA expression decreased by 35%, while HIF-1α mRNA expression increased 400%. These data suggest that regulation of Arnt and HIF-1α mRNA expression may contribute to the physiological responses of the heart during prolonged hypoxia.