Aim To study on the three polymorphic sites of apolipoprotein B gene Ecoli, Mspl and Xbal and their association with atherosclerosis in Chinese Han nationality. Methods Subjects were 84 patients of myocardial infraction (MI) and 84 normal matched controls. Polymorphisms of apo B gene were determined by using polymerase chain reaction technique. The plasma lipid were performed, TC were measured by enzymatic method, TG were measured by ethylene acetone micro method, HDLC was determined after phosphotungstate precipitation, LDLC was measured by polyvinyl sulfate precipitation method, apoAI and apo B were quantified by immunonephrometry and the determination of Lp(a) was performed with ELISA (enzyme linked immunosorbent assay). Results In Chinese Han population, the appearance of E+ and M- were frequent ones at EcoRI and MapI restriction sites in apoB gene (the frequencies were 0.945 and 0.969 respectively); comparatively, relative frequencies of E- and M+ alleles were only 0.056 and 0.081 respectively, which were significantly lower than in the White. The relative frequency of X+ allele at Xbal restriction site in apoB gene was significantly higher in the MI group than that in the control group ( the frequencies were 0.0774 and 0.0297,(P<0.05). The levels of TC, TG, LDLC, apoB, Lp(a) and the ratio of LDLC/HDLC, (TC-HDLC/HDLC) were significantly higher; and the level of HDLC, the ratio of apoAI/B were significantly lower in MI patients as compared with those of controls (P<0.05).The incidence of hyperlipidemia in MI group was 72% higher than control group (P<0.05), But the three polymorphic sites of apo B were not associated with the variation of the levels of lipid, lipoprotein and apolipoprotien. Conclusion The data suggested that allele of X+ at Xbal restriction sites in apoB gene was associated with susceptibility to coronary atherosclerosis.