Despite accumulating evidence supporting the association between variants of the ALOX5AP gene and atherosclerotic vascular events, the precise mechanism is still unclear. No variants in the coding sequence that lead to amino acid substitution have been found. We investigated genetic variants in the promoter region of the ALOX5AP gene and the association with ischemic stroke in a north Chinese Han population.505 cases of ischemic stroke and 500 age- and gender-matched controls of the north Chinese Han population were enrolled. Genetic variants in the promoter region of the ALOX5AP gene were identified by polymerase chain reaction and DNA sequencing. 40 cases and 40 controls were randomly selected and compared for serum leukotriene B(4) (LTB(4)) concentration. The effect on ischemic stroke was evaluated by logistic regression.Three genetic variants were identified, including a mutation (-519 G > A), an insertion and deletion polymorphisms (-581_582 Ins A) and a single nuclear polymorphisms (-946 A > G). Association study showed that the II genotype of -581_582 Ins A was significantly associated with ischemic stroke of a large artery atherosclerosis (OR = 3.50, 95% CI = 1.93-6.36, p = 0.0002) and undetermined etiology (OR = 3.66, 95% CI = 1.92-6.94, p = 0.0006). No significant association was found between the -519 GA genotype (OR = 0.35, 95% CI = 0.02-5.88, p = 0.46), -946 AG genotype (OR = 1.35, 95% CI = 0.85-2.16, p = 0.21) and ischemic stroke. There was no significant difference in serum LTB(4) concentration between cases (n = 40) and controls (n = 40) (log serum LTB(4) of cases vs. controls: 2.67 ± 0.14 vs. 2.73 ± 0.18 pg/ml, p = 0.10). However, the serum LTB(4) concentration was significantly higher in participants with the II genotype of -581_582 Ins A (n = 12) than that of participants with the DD genotype (n = 68) (log serum LTB(4) of participants with II genotype vs. DD genotype: 2.82 ± 0.18 vs. 2.68 ± 0.15 pg/ml, p = 0.01).The -581_582 Ins A polymorphism might be a novel genetic risk factor for ischemic stroke in a north Chinese Han population. Further studies on molecular mechanism are warranted.