Aim To study the genotype distribution of PON1 rs662, ABCB1 rs1045642 in patients with acute minor stroke, and its effect on short-term prognosis. Methods Acute minor stroke patients were included who were admitted to the Department of Neurology, the First Affiliated Hospital of Xinjiang Medical University from September 2018 to June 2019. The genotypes of PON1 rs662 and ABCB1 rs1045642 were detected by digital fluorescence molecular hybridization, and the stroke recurrence were evaluated by follow-up after 3 months and 6 months respectively. The association between these gene polymorphism and stroke recurrence was also investigated. Results There was a difference in the distribution of ABCB1 rs1045642 genotypes among different races. There were more mutant homozygous types in Uygur population (42.8%). After 3 months follow-up, a total of 7 of the 150 patients had terminal events, including 5 patients with transient ischemic attack (TIA) and 2 patients with recurrent ischemic stroke. The risk of recurrence at 3 months after stroke with PON1 and ABCB1 homozygous mutations was not yet considered to be increased. After 6 months follow-up, a total of 21 of the 124 patients had endpoint events, including 14 patients with recurrent TIA and 7 patients with recurrent ischemic stroke. PON1 mutant type had a higher recurrence rate than the wild type and mutant heterozygous type after 6 months(OR=3.4,5%CI 1.384～10.404, P=0.016). Conclusion The distribution of each genotype of ABCB1 rs1045642 is different between Uyghur and Han, and there are more mutant homozygous (TT) genotypes in Uyghur population. PON1 mutation has a high recurrence rate of ischemic events, which is a risk factor for recurrence 6 months after acute minor stroke.