Background: Apolipoprotein E (ApoE) and solute carrier organic anion transporter family member 1B1 (SLCO1B1) are involved in regulating lipid metabolism. However, the relation between genetic polymorphisms of APOE and SLCO1B1 and cerebral infarction (CI) remains unclear.Methods: A total of 945 CI patients and 1,028 control participants were included in the study. The single nucleotide polymorphisms (SNPs) rs429358, rs7412 of APOE gene and SNPs rs2306283, rs4149056 of SLCO1B1 gene were analyzed by fluorescence polymerase chain reaction (PCR) method.Results: The genotype ɛ3/ɛ3 is the most common genotype of APOE gene, in which ɛ3 is the allele with greatest frequency, followed by ɛ4 and ɛ2. There were statistically significant differences of genotype ɛ2/ɛ2 (c2=4.718, P=0.030), ɛ2/ɛ3 (c2=18.076, P<0.001), ɛ3/ɛ4 (c2=18.714, P<0.001), ɛ4/ɛ4 (c2=4.710, P=0.046) in CI patients comparing with controls. The SLCO1B1 genotype *1b/*1b and haplotype *1b have greatest frequency in the study sample. There was no statistically significant difference in frequencies of SLCO1B1 genotypes and haplotypes in CI patients comparing with controls. Moreover, the ε4 carriers had significantly higher LDL-C, Apo-B, and lower Apo-A1/Apo-B than the other groups, while the ε2 carriers showed the opposite results in the CI group and controls. Logistic regression analysis indicated that participants with ε4 allele had a significantly higher risk of CI in males (OR 3.508, 95% CI 2.186-5.629, P<0.001) and females (OR 2.723, 95% CI 1.428-5.194, P=0.002).Conclusions: The study indicated that the SNPs rs429358 and rs7412 of APOE may be associated with susceptibility to cerebral infarction, in southern Chinese Hakka population.