Aim To investigate cholesterol-induced atherogenesis molecular mechanism, clone and analyse the differentially expressed genes in vascular endothelial cell induced by cholesterol. Methods Suppression subtractive hybridization (SSH) method is used to isolate the differentially expressed cDNA in human umbilical vein endothelial cell induced by cholesterol. After sequencing and homology analysis, ten differentially expressed cDNA fragments are selected and analysed by reverse transcription-polymerase chain reaction(RT-PCR). Results Twenty-three differentially expressed cDNA fragments have been isolated. Seventeen of them are known genes, the other six are unknown genes. The known genes include thrombospondin-1, proteasome subunit (type and so on). The ten elective cDNA fragments (including four known genes and six unknown genes) that are identified by RT-PCR have the same expressed tendency as SSH discovery. Six differentially expressed unknown cDNA fragments have been accepted by GenBank as novel expressed sequence-tags (EST). Conclusion The high level expression of thrombospondin-1 and the low level expression of proteasome subunit (type) in endothelial cell induced by cholesterol may be related to cholesterol-induced atherogenesis.