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The aim of the present study was to investigate the correlation between the -1562C/T polymorphism in an intron of the matrix metalloproteinase-9 (MMP-9) gene and hemorrhagic transformation of ischemic stroke (IS). Using polymerase chain reaction-restriction fragment length polymorphism, the -1562C/T polymorphisms in 222 patients with IS were detected. The patients were divided into hemorrhagic transformation (HT; 84 cases) and non-hemorrhagic transformation (NHT) groups (138 cases) depending on the results from the susceptibility-weighted magnetic resonance imaging, which was performed between one and two weeks following stroke onset. The allele frequencies were subsequently compared. Baseline data of the two groups were comparable. The HT group exhibited a significantly lower frequency of the CT+TT genotype compared with the NHT group (17.86 vs. 30.43%, P<0.05). In addition, the frequency of T allele was significantly lower in the HT group compared with the NHT group (8.93 vs. 15.94%, P<0.05). Therefore, the results indicated that the -1562C/T polymorphism in the MMP-9 gene is correlated with hemorrhagic transformation of IS in the population studied. Furthermore, the T allele may be a protective factor for hemorrhagic transformation of IS in this population.