Linkage/linkage-disequilibrium analysis studies, based on positional information and gene function, indicated that ALOX5AP gene was an independent risk factor of cerebral infarction in humans; however, this needs to be verified among different populations. Herein, we verified whether ALOX5AP was a risk factor of cerebral infarction in the Chinese Han population. For this purpose, 547 cerebral infarction patients were enrolled as the case group; the control group comprised 794 healthy, age-matched individuals unrelated to case group and had no history of cerebral infarction/transient ischemic attack. Regarding single-nucleotide polymorphism (SNP) selection and ALOX5AP genotyping, we selected four SNP loci (SG13S25, SG13S114, SG13S89, and SG13S32) and determined allelic frequencies. Genotyping of SG13S114 and SG13S32 adopted a method of combining real-time quantitative PCR and allele-specific PCR. A linkage-disequilibrium analysis of ALOX5AP was also performed. We found that the allelic frequencies of SG13S25 and SG13S89 were below 5% and those of SG13S114 and SG13S32 were above 5%. We did not find any differences between the case and control groups regarding allele, allele types, and haplotype gene frequencies of two SNP loci. The results indicate that the two genetic polymorphisms of ALOX5AP, SG13S114 and SG13S32, are not associated with cerebral infarction in Chinese Han population.