Aim To sreen differential genes associated with coronary heart disease in Uygur, Kazakh, and Han population of Xinjiang using gene microarray expression profiles. Methods A case-control study including 9 cases (3 cases in Uygurs, 3 cases in Kazakhs, and 3 cases in Hans) with coronary heart disease confirmed by coronary angiography and 9 gender-, age-, and ethnic-matched normal controls was designed for the present study. Human whole genome expression microarray was used to screen differential genes associated with coronary heart disease. Results 33 genes associated with coronary heart disease were differentially expressed, 26 genes associated with coronary heart disease in Han population were differentially expressed, 2 genes associated with coronary heart disease in Uygur population were differentially expressed, while the differentially expressed genes were not screened in Kazakh population. Through GO and Pathway analysis, the differentially expressed genes were related to immune response. Conclusion The results of gene microarray screening showed that the differentially expressed genes were mainly related to immune response.