Intermittent hypoxia (IH) occurs in many pathological conditions including recurrent apneas. Hypoxia-inducible factors (HIFs) 1 and 2 mediate transcriptional responses to low O 2 . A previous study showed that HIF-1 mediates some of the IH-evoked physiological responses. Because HIF-2␣ is an orthologue of HIF-1␣, we examined the effects of IH on HIF-2␣, the O2-regulated subunit expression, in pheochromocytoma 12 cell cultures. In contrast to the up-regulation of HIF-1␣, HIF-2␣ was down-regulated by IH. Similar down-regulation of HIF-2␣ was also seen in carotid bodies and adrenal medullae from IH-exposed rats. Inhibitors of calpain proteases (ALLM, ALLN) prevented IH-evoked degradation of HIF-2␣ whereas inhibitors of prolyl hydroxylases or proteosome were ineffective. IH activated calpain proteases and down-regulated the endogenous calpain inhibitor calpastatin. IH-evoked HIF-2␣ degradation led to inhibition of SOD2 transcription, resulting in oxidative stress. Over-expression of transcriptionally active HIF-2␣ prevented IH-evoked oxidative stress and restored SOD2 activity. Systemic treatment of IH-exposed rats with ALLM rescued HIF-2␣ degradation and restored SOD2 activity, thereby preventing oxidative stress and hypertension. These observations demonstrate that, unlike continuous hypoxia, IH leads to down-regulation of HIF-2␣ via a calpain-dependent signaling pathway and results in oxidative stress as well as autonomic morbidities.calcium signaling ͉ hypoxia inducible factors S leep-disordered breathing with recurrent apneas is a leading cause of morbidity and mortality affecting an estimated 18 million people in the United States alone (1-4). Recurrent apneas are characterized by transient, repetitive cessations of breathing (Ϸ10 sec in adults) resulting in periodic decreases in arterial blood O 2 or intermittent hypoxia (IH). Patients with recurrent apneas are at risk for developing several comorbidities including hypertension, sympathetic activation, breathing abnormalities, atherosclerosis, and stroke (4-8). Exposure of rodents to IH alone induces several co-morbidities reported in patients with recurrent apnea (9-11). However, little information is available on the molecular mechanisms underlying the morbidities associated with IH.Hypoxia-inducible factors (HIFs) mediate transcriptional responses to low O 2 (12). HIF-1 is the prototypical member of the HIF family and comprises an O 2 -regulated ␣ subunit and a constitutive  subunit (13). HIF-1 transcriptional activity is induced under continuous hypoxia (CH) as a result of HIF-1␣ protein accumulation resulting from decreased O 2 -dependent proline hydroxylation, ubiquitination, and proteasomal degradation (14). Recent studies showed that IH leads to HIF-1␣ accumulation and utilizes signaling pathways distinct from those identified with CH (15). The importance of HIF-1 to IHassociated physiological and pathophysiological responses was studied in mice with heterozygous deficiency of HIF-1␣. IHevoked cardio-respiratory and metabolic morbidities were absent ...