Objective:To explore the single nucleotide polymorphism (SNPs) of 5-lipoxygenase activating protein(ALOX5AP) and phosphodiesterase 4D (PDE4D) genes on cerebral infarction,and if there is a relationship between the genes and susceptibility to cerebral infarction in the population of Nanjing city of Jiangsu Province. Methods:A total of 280 consecutive patients with Lacunar infarction(LI) and 258 population-based controls that had been matched for age and sex were examined using a case-control design. Four SNPs covering those two genes were genotyped with ligase detection reaction(LDR) and multiplex polymerase chain reaction(PCR). Results:All alleles and genotypes were similar between cases and controls in PDE4D,and no significant association with LI was revealed by haplotype anaylsis. However,both rs4073259 and rs4769055 in ALOX5AP were found to be associated with LI(P < 0.05). The GA haplotype was related to a significantly increasing risk of LI,and the GC haplotype showed an association with decreasing risk of LI(P < 0.01). Conclusion:The present study suggested that variants in the PDE4D gene were not the risk factors for LI in individuals from Nanjing city in Jiangsu Provinces. However,ALOX5AP might be involved in the incidence of LI in the Nanjing population.