Matrix metalloproteinases (MMPs) are proteolytic enzymes capable of degrading extracellular matrix. Their role has been emphasized in tumor invasion, metastasis and tumor-induced angiogenesis. The gene encoding MMP-3 is polymorphic and an insertion (6A)/deletion (5A) polymorphism (5A/6A polymorphism) in the MMP-3 gene may have functional significance in the regulation of its expression. In the present work the distribution of genotypes and frequency of alleles of the 5A/6A polymorphism in subjects with ovarian cancer were investigated. Paraffin embedded tumor tissues were obtained from 118 postmenopausal women with node-negative and node-positive ovarian cancer. The 5A/6A polymorphism was determined by PCR amplification using the allele specific primers. The distribution of the genotypes of the 5A/6A polymorphism in both control and study patients did not differ significantly (p>0.05) from those predicted by the Hardy-Weinberg distribution. There were no significant differences (p>0.05) in genotype distributions and allele frequencies between subgroups assigned to histological stage. The results suggest that the 5A/6A polymorphism of MMP-3 gene may not be linked with appearance and/or progression of ovarian cancer.