Pulmonary hypertension (PH) is a major cause of death and impairment of quality of life. Chronic exposure to hypoxia alone is sufficient to cause major structural changes to pulmonary arteries (Groves et al., 1987), as well altering the biochemical and functional phenotypes of all of the vascular cell types. Furthermore, these hypoxia-induced changes are site specific and vary between the large and small vessels of the pulmonary vasculature. Although traditionally it has been stated that PH is a disease of distal lung circulation, more current research has shown that structural changes in larger vessels contribute directly to right ventricular work and failure thus changing blood flow within the smaller vessels (Stenmark & Mecham, 1997). In order to determine which genes are involved in this remodelling process, we have utilized an affymetrix gene chip array to determine the gene expression profile of human pulmonary artery smooth muscle cells (HPASMC) cultured for 24 hours under nonhypoxic (pO2≈ 150 mmHg) and hypoxic conditions (pO2≈ 7 mmHg). Analysis for differential gene expression was done using the Welch t-test, the Baysian t-test and the moderated t-test. Only probe sets which passed all three statistical tests and showed either a 1.5 fold increase or 1.5 fold decrease in expression were chosen for further investigation. Of the 188 individual genes which met these criteria, 133 showed an increase in expression in response to chronic hypoxia and 47 genes were downregulated. The gene chip array data was validated by performing quantitative PCR on a random selection of genes which were shown to be altered by chronic hypoxia. As smooth muscle cells are known to differentiate quickly, HPASMC of the same passage were stained with α-smooth muscle actin to show that they had the correct phenotype when the experiments were performed. Furthermore, HPASMC were also shown to respond to the vasoactive peptide Endothelin-1 in calcium imaging experiments, which is another indicator of smooth muscle function (Sinha et al., 2006). The largest category of genes which were regulated by hypoxia were proteins involved in metabolism, of which many have previously been reported to be regulated by hypoxia inducible factor 1α (HIF-1α). In addition, numerous proteins involved in collagen synthesis, cell proliferation / motility, oxidoreduction and solute transportation were differentially expressed. These results suggest that in addition to the effect that vasoactive substances released from the endothelium have on the contractile and proliferative state of smooth muscle cells (Aaronson et al., 2002), hypoxia can directly regulate genes within HPASMC which are important in responding to injury.