Aim To study the large amount of differentially displayed genes and expressed sequence-tags (EST) obtained by gene clone is a difficult problem. It is important to exploit new methods for further study. Methods EST were acquired from human umbilical vein endothelial cells induced by cholesterol by suppression subtractive hybridization (SSH). Bioinformatics analysis of atherosclerosis related genes was done by the bioinformatical databases and bio-softwares such as BLAST, ExPasy analyse soft box, DNAMAN soft, BioEdit soft and RasMol soft. Results We obtained a 684 bp complete cDNA sequence by electronic clone, which was homogeneous to cytochrome C oxidase subunit Ⅱ gene (COX2). The complete genome of COX2 sited in homo sapiens mitochondrion, and included a complete open reading frame (ORF) coding 227 amino acids. The analysis of its protein sequence indicated that COX2 gene encode a 25.6 kDa protein, which was a weak acid signal anchor. The three-dimensional structure of COX2 was a representative chair-like stucture, containing a hydrophobicity region, a transmembrane domain and a periplasmic domain. The periplasmic domain of the COX2 protein sequence was high conservative in the process of evolutions by the analysis of the protein evolutions. Conclusion We obtained the information of COX2 about nucleic acid sequence and protein sequence by bioinformatics analysis