Objective: To investigate the differential gene expression profiles in patients with blood stasis syndrome by oligonucleotide microarray technique.Methods: Sixteen patients with blood stasis syndrome were divided into patients with coronary heart disease (CAD) (n=8) and non-CAD patients (n=8) by using coronary angiography. The sex- and age-matched eight healthy persons were enrolled as control group. Venous bloods were collected for extracting RNA. Test-3 chip was first employed to examine the quality of samples. Then the samples were hybridized with Affymetrix U133 Plus 2.0 array to compare the gene expression profiles among the three groups. Gene-array scanner and gene chip operating software were applied to screen hybridization signals and analyze gene expression respectively. Based on the comparison of the three groups of samples, the differential genes related with blood stasis syndrome were analyzed by Gene Ontology (GO) and pathway, and confirmed by real-time reverse transcription polymerase chain reaction (RT-PCR).Results: Forty-eight differential genes were found being associated with blood stasis syndrome, including 26 up-regulated genes and 22 down-regulated genes. Five of the forty-eight genes (10.4%) were related to inflammatory reaction and immune response through the GO analysis. In the pathway analysis, five of ten significant pathways were referred to inflammation and immune response. The results of real-time RT-PCR proved the accuracy of the gene chip.Conclusion: Inflammatory- and immune-related genes have a remarkable predominance in blood stasis syndrome gene expression profiles, which may explain the function of inflammation and immune response in the occurrence and development of blood stasis syndrome.