Aim To investigate gene expression patterns of atherosclerosis (As) induced by intermittent hypoxia. Methods The total RNA were extracted from the aorta of rabbits and then reverse transcribed to make the probe. The probes hybridisate the gene chip from Afymetrix's company, the result signals were scanned by ScanArray HS-038 and analyzed by Microarray Suite Version 5.0. Results There was total 187 genes down-regulated or up-regulated, classified by cell signal transduction, immunology inflammatory response, extracellular matrix degrade, cell apoptosis, smooth muscle cell related, oncogene or tumor suppressor and cell migration. The expression level of cyclooxygenase-2 (COX-2) mRNA in abdominal aorta was significantly associated with the change of abdominal aorta endarteropathy (P<0.05) . Conclusion The process of As induced by intermittent hypoxia is correlated to many genes, gene chip, the high-flux detecting technique can provide the new ideas for the mechanism research of As. COX-2 plays an important role in As.