In this study, we analyzed the transcribed regions and splicing sites of the MSX1 and MSX2 genes in a large cohort of CHD patients and controls, and found that the variations rs3821949 and rs12532 in the MSX1 gene were associated with the risk of CHD in the Chinese Han population, demonstrating the involvement of the MSX1 gene in the CHD etiology. This evidence concerns the gene MSX1 and coronary artery disorder.