Objective Risk genotypes of patients with ischemic stroke were analyzed to provide evidence for clinical prevention. Methods Fluorescence staining in situ hybridization karyotype analysis was performed on 92 patients with ischemic stroke hospitalized in the department of Neurology of our hospital. Genes associated with the risk of ischemic stroke were examined in 36 healthy subjects: Methylene Tetrahydrofolate Reductase(68MTHFR, 677C>T), V factor Leiden(187F5, 41721G>A), Plasminogen activator inhibitor-1(27PAI-1, 4G/5G). Genotype distribution and allele frequency were compared between the two groups. Results The distribution of heterozygous and homozygous mutant 27 and 68 genes in ischemic stroke group was higher than that in normal control group, the difference was statistically significant(P<0.05). Allele frequency of ischemic stroke group was significantly higher than that of control group(P<0.01). The distribution of 187 genotypes and allele frequency of two groups were compared, the differences were not statistically significant(P>0.05). Conclusion Pai-1 effector molecule (locus 27) is the key genotype for ischemic stroke, and the mutations in MTHFR metabolic enzymes(site 68) increase the risk of stroke; the V factor Leiden(187) had few mutations in the tested population, there was no conclusive effect on the risk of ischemic stroke.