Aim To determine the genes involved in the mechanisms of LDL oxidation mediated by endothelial cells. Methods Microarray analysis on human signal transduction associated proteins was applied to profile changes in gene expression of human ECV304 endothelial cells induced by low density lipoprotein. Results In 1 990 genes detected,52 genes were identified to be >2-fold difference in expression, among which 23 genes with elevated expression and 29 genes with reduced expression. Some of these 52 genes encoding proteins have been determined to be correlated with atherosclerosis. Conclusion Those genes expressed differently may provide new insights into the possible mechanisms of low density lipoprotein oxidation mediated by endothelial cells.