Behçet's Disease (BD) is a systemic immunoinflammatory disease. The pathogenesis of BD is unknown, although raised levels of several pro-inflammatory cytokines have been reported. Nuclear factor kappa B (NF-kappaB) is a family of critical transcriptional factors involved in the regulation of a large variety of inflammatory responses and apoptosis. In this study we investigated the -94 insertion/deletion ATTG promoter polymorphism of the NF-kappaB1 gene (NFKB1) in 86 patients with BD and 100 healthy controls. The frequency of the -94ins ATTG (I) allele was 61.6% in patients with BD and 59% in controls and the frequency of the -94 del ATTG (D) allele was 38.4% in patients with BD and 41% in controls. The frequency of the -94ins ATTG (I) allele was significantly higher in patients with ocular involvement (P = 0.03). In the genotype study, the overall frequencies of II, ID and DD were 40.7%, 41.9%, and 17.4% in the patient group and 30%, 58% and 12% in the control group (P: 0.08). The II genotype was significantly higher in patients with ocular involvement, genital ulcers or papulopustular lesions. The frequency of the II, ID and DD genotypes showed no marked difference in patients with erythema nodosum, pathergy positivity, arthritis or vascular involvement. No difference was found for gender, positive family history or age at disease onset. This study provides evidence that the -94ins/del ATTG promoter polymorphism of NFKB1 may have functional consequences in BD, especially in patients with ocular involvement.