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Background: Several genetic factors underlying ischemic stroke have been identified. Variants of Neuropeptide Y (NPY), whose product plays diverse roles in modulating physiological functions, have been associated with an increased risk of ischemic stroke in South Korean individuals. Aims: We explored the association between a polymorphism in the NPY gene promoter at position -399 and the risk of ischemic stroke in Han Chinese. Study Design: Case-control study. Methods: The polymorphism -399T/C in the promoter of NPY was analysed in 500 patients with ischemic stroke and 500 healthy individuals by amplification and sequencing of this region. Non-conditional logistic regression was used to analyse association between genotypes and the risk of ischemic stroke. Results: Genotype and allele frequencies differed significantly between the ischemic stroke and control groups (P<0.05). Additionally, compared to stroke patients with the TT genotype, those with the CC genotype had a 1.7-times higher risk of ischemic stroke (OR=1.739, 95%CI=1.201-2.520, P=0.003), especially for those who were over 60 years old or male. Individuals with the TC genotype did not have an increased risk of ischemic stroke (P>0.05). Conclusion: The -399T/C polymorphism of the NPY gene is associated with ischemic stroke in Han Chinese individuals, and the CC genotype may be a risk factor for ischemic stroke.