Aim To clone and isolate the altered expression genes induced by atherogenic factor will improve our understanding the molecular mechanism in atherosclerosis. Methods Modified differential display-PCR method was used to clone the differential expressed genes in cultured vascular endothelial cells stimulated by oxidized low density lipoprotein. Northern blot analysis was chosen to verify the results. Results One up-regulated cDNA band was found in oxidized low density lipoprotein induced human umbilical vein endothelial cells. It is 283 bp in length and 100% homologous to human thymosin β4 in sequence. It also contain the complete open reading frame. Thymosin β4 was up-regulated 3-fold in oxidized low density lipoprotein induced human umbilical vein endothelial cells. Thymosin β4 was a differentiation molecular for many cells and is involved in angiogenesis. Conclusions Our results first show that oxidized low density lipoprotein can stimulate the high expression of thymosin β4 in vascular endothelial cells and may be regulate the proliferation, differentiation of vascular endothelial cells. The modified differential display technique has the characteristics of convenience, high specificity and reproducibility.