Hypoxia inducible transcription factor (HIF)-1alpha plays an important role in the development of hypoxic pulmonary hypertension, but little is known about HIF-2alpha and HIF-3alpha with respect to transcriptional regulation by hypoxia. To examine the expression patterns of all HIF-alpha subunits (HIF-1alpha, HIF-2alpha and HIF-3alpha) in pulmonary arteries of rats undergoing systemic hypoxia, five groups of healthy male Wistar rats were exposed to normoxia (N) and hypoxia for 3 (H3), 7 (H7), 14 (H14) and 21 (H21) d respectively. Mean pulmonary arterial pressure (mPAP), vessel morphometry and right ventricular hypertrophy index were measured. Lungs were inflation fixed for immunohistochemistry and in situ hybridization, and homogenized for Western blot. mPAP increased significantly after 7 d of hypoxia [(18.4+/-0.4) vs. (14.4+/-0.4) mmHg, H7 vs. N], reached its peak after 14 d of hypoxia, then remained stable. Pulmonary artery remodeling and right ventricular hypertrophy developed significantly after 14 d of hypoxia. During normoxia, HIF-1alpha and HIF-3alpha staining were slightly positive regarding mRNA levels. A substantial alteration of HIF-1alpha and HIF-3alpha staining occurred in pulmonary arteries after 14 d and 7 d of hypoxia, respectively, but HIF-2alpha staining showed an inversed trend after 14 d of hypoxia. Protein levels of all HIF-alpha subunits except HIF-3alpha showed a marked increase corresponding to the duration of hypoxia, which was obtained by Western blot. Our study found that HIF-1alpha, HIF-2alpha and HIF-3alpha may not only confer different target genes, but also play key pathogenetic roles in hypoxic-induced pulmonary hypertension.