Behçet’s Disease is a chronic, relapsing-remitting autoinflammatory syndrome with a strong HLA-B*51 association. In this paper, we describe a human cohort of 267 individuals with Behçet’s Disease and 445 matched controls from a tertiary referral centre in the United Kingdom. HLA-B*51 was confirmed as a genetic risk factor in this group (P=0.0006, Pc=0.0192, OR 1.92, 95% CI 1.33–2.76). KIR3DL1/S1 allele-level analysis indicated that low-expressing KIR3DL1/S1 alleles in combination with KIR3DS1 increased the risk of developing Behçet’s Disease (KIR3DL1LOW/KIR3DS1: P=0.0004, Pc=0.0040, OR 2.47, 95% CI 1.43–4.25), whereas high-expressing KIR3DL1/S1 alleles in combination with a null-expressing KIR3DL1 reduced the risk of disease (KIR3DL1HIGH/KIR3DL1NULL: P=0.0035, Pc=0.0350, OR 0.53, 95% CI 0.33–0.87). Behçet’s Disease can manifest as a purely mucocutaneous disease or can involve other organ systems such as the eyes. In the UK cohort studied here, KIR3DL1LOW/KIR3DS1 increased the risk of ophthalmic disease (P=1.2×10–5, OR 3.92, 95% CI 2.06–7.47), whereas KIR3DL1HIGH/KIR3DL1NULL reduced the risk of having purely mucocutaneous disease (P=0.0048, OR 0.45, 95% CI 0.25–0.81). This is the first analysis of KIR3DL1/S1 allelic variation in Behçet’s Disease and may provide insight into the pathogenic role of HLA-B*51 and its interaction with KIR3DL1/S1.