Matrix metalloproteinase (MMP)-9 expression is reported to be upregulated in several primary vasculitides. The -1562C>T and -91 [CA](n) repeat polymorphisms can affect MMP-9 promoter activity. We investigated the distributions of these functional polymorphisms in 122 patients with Behçet's disease (BD) and in 122 gender- and age-matched healthy controls. Plasma levels of MMP-9 were analyzed. The frequency of "L" alleles with [CA](n) <21 was significantly lower in all BD patients (vs controls, odds ratio (OR) = 0.371 [95% confidence interval 0.152-0.905]) and male patients (vs male controls, OR = 0.117 [0.019-0.737]). Furthermore, the frequency of "H/H" homozygote with [CA](n) > or = 21 was significantly higher in BD patients than controls (OR = 2.677 [1.065-6.729]). Moreover, the frequency of CL haplotype with lower promoter activity was significantly lower in BD patients (vs controls, OR = 0.374 [0.149-0.939]) and in BD patients with visceral involvement (OR = 0.202 [0.044-0.916]). Although plasma MMP-9 levels were not different between controls and BD patients, concentrations of this substance were significantly higher in male patients (vs male controls, p = 0.044) or patients with visceral involvements (vs patients without visceral involvement, p = 0.027). These results suggest that MMP-9 is a novel susceptibility gene and its promoter polymorphisms can affect the development of visceral involvement in BD.