Several genetic factors seem to be involved in the pathogenesis of rheumatoid arthritis (RA). The aim of this study was to analyze whether functional polymorphisms in the promoter region of the MMP-1, -3 and -9 genes were associated with RA. The study population comprises 110 RA patients and 100 healthy controls. The -1607 1G/2G MMP-1, -1171 5A/6A MMP-3, and -1562 C/T MMP-9 polymorphisms were analyzed. The frequency of the 5A allele of MMP-3 gene was significantly higher in the controls when compared with the RA patients (0.45 vs. 0.32, P < 0.01). No significant differences were observed in the allele frequencies for the MMP-1 and -9 polymorphisms between RA patients and controls. Individuals carrying MMP-3 5A allele have significant higher frequency of extra-articular manifestations and rheumatoid nodules than individuals homozygous for 6A allele (P < 0.05). The results presented in this study provide evidence of an association between the MMP-3 gene polymorphism and RA.