Behçet's disease is a chronic systemic inflammatory disorder characterized by four major manifestations: recurrent ocular symptoms, oral and genital ulcers and skin lesions. We conducted a genome-wide association study in a Japanese cohort including 612 individuals with Behçet's disease and 740 unaffected individuals (controls). We identified two suggestive associations on chromosomes 1p31.3 (IL23R-IL12RB2, rs12119179, P = 2.7 × 10⁻⁸) and 1q32.1 (IL10, rs1554286, P = 8.0 × 10⁻⁸). A meta-analysis of these two loci with results from additional Turkish and Korean cohorts showed genome-wide significant associations (rs1495965 in IL23R-IL12RB2, P = 1.9 × 10⁻¹¹, odds ratio = 1.35; rs1800871 in IL10, P = 1.0 × 10⁻¹⁴, odds ratio = 1.45).