Objective To investigate the association between 1612 (5A/6A) polymorphism of MMP3 gene and acute ischemic stroke (AIS). Methods SNaP shot minisequencing was used to study whether there was a significant difference in MMP3-1612 genotype and allele frequency between 300 AIS patients and 300 healthy controls. The AIS cases were divided into five subtypes: large-artery atherosclerosis (LAA), small-artery occlusion (SAO), cardioembolism (CE), stroke of other determined etiology (SODE) and stroke of other undetermined etiology (SUE). The differences in MMP3-1612 genotype and allele frequency were studied among the five subtypes. Results For the MMP3 gene-1612 (5A/6A) polymorphism, 5A/5A genotype was significantly increased in the AIS group as compared to the control group (P < 0.05). 5A/5A genotype of MMP3 promoter was significantly increased in the LAA subtype of AIS (P < 0.05). Multiple stepwise logistic regression analysis showed that the 1612-5A/6A polymorphism of MMP3 gene was significantly associated with AIS after adjustion of the conventional risk factors. Conclusions The 1612 polymorphism of MMP3 gene is associated with acute ischemic stroke, the 5A/5A genotype may be the risk factor of acute ischemic stroke. The mechanism may be related to arteriosclerosis. But large samples will be studied to confirm our conclusion.