Matrix metalloproteinases (MMPs) play important roles in cancer invasion and metastasis. Recently, functional gene polymorphisms in the promoter regions of MMP-1 1G/2G, MMP-3 5A/6A and MMP-9 C/T have been found, and have been reported to be associated with the prognosis of various cancers. In this study, we examined the association of the MMP-1, -3, -9 genotypes with the prognosis of hepatocellular carcinoma (HCC).Ninety two patients with hepatitis C virus related HCC were enrolled in the study. Genomic DNA samples were extracted from peripheral white blood cells, and gene polymorphisms of MMP-1, MMP-3and MMP-9 were analyzed by PCR-RFLP methods.There were no significant differences of the survival rate between MMP-1 1G carriers and 2G homozygotes, and between MMP-9 T carriers and C homozygotes. By contrast, HCC patients with MMP-35A allele had a significantly poorer prognosis than 6A homozygotes.Unlike MMP-1 and MMP-9 genotypes, MMP-3 5A allele, with higher transcriptional activity, may be a risk factor for the poor prognosis of HCC patients.