Biliary atresia (BA) is an inflammatory obliteration cholangiopathy, leading to progressive fibrosis and cirrhosis. Adiponectin, an inflammatory adipokine, is associated with liver fibrosis and inflammation, further suggesting that it may be associated with pathogenesis of BA. In this study, we examined whether two SNPs of adiponectin (+45T/G and +276G/T) were associated with the risk factors of BA. Total of 106 Thai patients with BA and 107 control subjects were included in this study. Adiponectin polymorphisms at +45T/G (rs2241766) of exon2 and +276G/T (rs1501299) of intron2 were evaluated by PCR-RFLP technique. Serum samples were assayed using enzyme-linked immunosorbent assay (ELISA). The +276G/T SNP, the frequency of GG genotype (P = 0.009) and G allele (P = 0.0043) were significantly associated with an increased risk of BA. In addition, adiponectin levels were significantly higher in BA patients (172.75 ± 90.85 ng/ml) than those controls (93.91 ± 53.35 ng/ml, P < 0.001). The +276G/T polymorphism was associated with adiponectin levels. The serum adiponectin concentrations were higher in BA patients with the GG genotype (197.94 ± 86.45 ng/ml) compared with GT (122.14 ± 78.45 ng/ml) and TT genotype (118.75 ± 84.47 ng/ml for TT, P < 0.001). Adiponectin gene variation showed an association with BA, and adiponectin genotype may predict the increasing risk for BA and play a role in the susceptibility and progression of BA.