Aim Atherosclerotic cerebral infarction (ACI) as agradually progressive atherosclerotic disorder has been thought be a hetero-ground and multifactor of environment, There are in different epidemiologic state. The relationship of ministellite region (MSR) polymorphisms at 3'-end of apolipoprotein B gene in Chinese ACI and healthy controls was observed. Methods The 3' hypervariableministellite region polymorphism of apolipoprotein B gene was examined by polymerase chain reaction technique in 84 patients with ACI and 107 age-matched Chinese healthy controls. The targeted ministellite region were amplified rapidly and accurately, and then identified oligonucleotide primer 5'-ATG GAA ACG GAG AAA TTTG-3',5'-CCT TCT CAC TTG GCA AAT AC-3' was used to the amplification of DNA genome which in peripheral leucocyte, number repeat unit (MSR) alleles detached by polyacrylamide gel electrophoresis (PAGE). Results ①The frequency distribution of apolipoprotion B 3'ministellite region alleles was in monomold peaks at 37, 39 repeat uints in both group(from MSR29 to MSR53), and the big number repeat unit (MSR39 is 18.5%, and P<0.02). ②The homozygote genotype of the big number repeat units alleles was related to the high level of apolipoprotein and LDL. The blood lipid parametes in differant zygote genotype of the small number repeat unit (MSRS, ≤MSR37) and big number repeat unit (MSRB, ≥MSR39 ) was cmparised (table 2), the homozygote big copied alleles (MSRB/MSRB) related to the increase of apo B and LDLC, There were same tandency in ACI and controls. Conclusions Our investigate resluts suggested the possibility that apolipoprotein B 3' gene ministellite region alleles polymorphism increase the susceptibility to atherosclerosis by means other than by altering lipoprotein levels deserves further consideration.