In the present study, we have observed a high prevalence of carotid atherosclerosis (43.2% [1,028/2377)] in the high-risk stroke population and the associations of variants in two distinct genes related to inflammation (IL1A rs1609682, PPARA rs4253655) and one gene related to endothelial function (HABP2 rs7923349) with carotid atherosclerosis in southwestern China. Here, HABP2 is linked to Stroke.