This study aimed to investigate the predisposition of common pre-miRNA SNPs with Behcet's disease (BD), Vogt-Koyanagi-Harada (VKH) syndrome and acute anterior uveitis (AAU) associated with ankylosing spondylitis (AS). A two-stage association study was carried out in 859 BD, 400 VKH syndrome, 209 AAU(+)AS(+) patients and 1,685 controls all belonging to a Chinese Han population. Genotyping, the expression of miR-196a and Bach1 (the target gene of miR-196a), cell proliferation, cytokine production were examined by PCR-RFLP, real-time PCR, CCK8 and ELISA. In the first stage study, the results showed significantly increased frequencies of the miR-196a2/rs11614913 TT genotype and T allele in BD patients (adjusted P(c) = 0.024, OR = 1.63; adjusted P(c) = 5.4 × 10(-3), OR = 1.45, respectively). However, no significant association of the tested SNPs with VKH and AAU(+)AS(+) patients was observed. The second stage and combined studies confirmed the association of rs11614913 with BD (TT genotype: adjusted P(c) = 6×10(-5), OR = 1.53; T allele: adjusted P(c) = 8×10(-6), OR = 1.35; CC genotype: adjusted P(c) = 0.024, OR = 0.68). A stratified analysis showed an association of the rs11614913 TT genotype and T allele with the arthritis subgroup of BD (P(c) = 5.3 × 10(-3), OR = 1.89; P(c) = 0.015, OR = 1.56, respectively). Functional experiments showed a decreased miR-196a expression, an increased Bach1 expression and an increased production of IL-1β and MCP-1 in TT cases compared to CC cases (P = 0.023, P = 0.0073, P = 0.012, P = 0.002, respectively). This study shows that a functional variant of miR-196a2 confers risk for BD but not for VKH syndrome or AAU(+)AS(+) by modulating the miR-196a gene expression and by regulating pro-inflammatory IL-1β and MCP-1 production.