In conclusion, the present study showed that leukocyte DNA methylation of the AMH, C17orf82, HDAC9, IGFBP3, LRRC10B, PDE3A, PRDM6, SYT7 and TBX2 genes was significantly associated with the risk of ischemic stroke and identified prospective associations between lower methylation levels of the PDE3A, AMH, C17orf82, PRDM6 and TBX2 genes and poor outcomes within 3 months of the onset of ischemic stroke. Here, HDAC9 is linked to ischemic stroke.