Objective To investigate the expression of hypoxia inducible factor 1 alpha (HIF 1α) and inducible nitric oxide synthase (iNOS) genes in rats’ pulmonary arteries in different phases of hypoxia induced pulmonary hypertension development Methods Models of chronic hypoxic pulmonary hypertension rat were duplicated by intermittent hypoxia Mean pulmonary arterial pressure (mPAP) was measured by right heart catheterization HIF 1α and iNOS messenger ribonucleic acid (mRNA) were detected by in situ hybridization HIF 1α and iNOS protein were measured by immunohistochemical analysis Results Expression of HIF 1α protein was upregulated in pulmonary arterial tunica intimae of all hypoxic rats In pulmonary arterial tunica media, the level of HIF 1α protein was markedly upregulated at days 3 and 7 of hypoxia ( P <0 01), then tended to restore at 14 days and 21 days HIF 1α mRNA levels in pulmonary arteries of rats began to increase significantly at day 14 of hypoxia ( P <0 01) Expression of iNOS mRNA and protein in pulmonary arteries of rats were upregulated by hypoxia for 3 days ( P <0 01), then reached its peak and maitained the same level while the extension of hypoxia Linear correlation analysis showed that iNOS protein was associated with both mean pulmonary arterial pressure ( r =0 74, P <0 01) and hypoxic pulmonary vascular remodeling ( r =0 78, P <0 01), whereas the inverse was associated with HIF 1α protein ( r =-0 52, P <0 01) Conclusions HIF 1α and iNOS are both involved in the pathogenesis of hypoxia induced pulmonary hypertension in rat HIF 1α protein may upregulate the expression of iNOS gene by transcriptional activation; in addition, iNOS protein may inhibit the expression of HIF 1α protein