Aim To investigate the association between matrix metalloproteinase-9 (MMP-9) polymorphism (C1562T) and coronary heart disease (CHD) in Han population of South China. Methods The study included 150 patients with acute coronary syndrome (ACS group), 110 patients with stable angina pectoris (SAP group) and 70 controls (control group) , all of which were confirmed by angiocardiography. Plasma levels of MMP-9 were measured by enzyme-linked immunosorbent assay (ELISA). Promoter C1562T gene polymorphism of MMP-9 was analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Genotype and allele frequency were compared among groups. Results Plasma MMP-9 level in ACS group were significantly higher than those of SAP group (p<0.05) and control group (p<0.01), however there was no difference between SAP group and control group (p>0.05). The frequency of CT and CT+TT genotype and T allele were higher in ACS group compared with those in control group and SAP group (p<0.05 or 0.01), but the frequencies of C/T genotypes and alleles were not statistically different between SAP group and control group (p>0.05). Plasma MMP-9 level of CT/TT genetype was higher than that of CC genetype (p<0.01). Conclusion The genetic polymorphism in MMP-9 promoter (C1562T) is associated with ACS in the Han population of South China, and T allele is a susceptible gene of unstability of atherosclerosis plaque.