Aim To investigate gene expression patterns of atherosclerosis (As) induced by homocysteine (Hcy). Methods Total RNA were isolated from peripheral blood lymphocytes of 3 inpatients who had no traditional risk factors of coronary heart disease (CHD). They were one with normal coronary angiography and plasma Hcy level, one CHD patient with normal plasma Hcy level, and one CHD patient with high plasma homocysteine level. The RNAs were reversely transcribed to the cDNAs to prepare the hybridization probes. The probes were hybridized to the gene chip with 1152 genes to study gene expression patterns. Results There were 177 differentially expressed genes between the CHD patient with high plasma homocysteine level and the patient with normal coronary angiography and plasma Hcy level (group 1). There were 151 differentially expressed genes between the CHD patient with high plasma homocysteine level and the CHD patient with normal plasma Hcy level (group 3). A parallel comparison between group 1 and group 3 gene chips showed that there were 48 differentially expressed genes in common, of which there were 25 down-regulated and 23 up-regulated genes. Conclusion Among the differentially expressed genes, some are involved in the functions of apoptosis, signal transduction, immunology, translation of protein and proto-oncogene, etc. They had potential values in genesis of As induced by Hcy. The study based on gene chip in researching the differentially expressed genes of As induced by Hcy will provide new clues for finding out the pathogenesis of As.