Objective To analyze the expression and significance of cadherin-11 (CDH11) in livers of children with biliary atresia (BA). Methods Fifty children with BA and eight children with choledochal cyst (CC) were selected as the research objects. The expression levels of CDH11 and liver fibrotic marker genes in the livers of the children were evaluated by quantitative real-time polymerase chain reaction. The correlation between CDH11 and liver fibrotic marker genes or serum liver function markers was analyzed. Results The mRNA levels of CDH11 were significantly elevated in livers of children with BA compared to children with CC (P< 0.01). Hepatic CDH11 mRNA levels were positively correlated with the expression levels of transforming growth factor beta 1, transforming growth factor beta 2, keratin 19, actin alpha 2, smooth muscle, collagen type I alpha 1 and collagen type IV alpha 1 in children with BA (r= 0.36 ~ 0.73, all P< 0.01). The mRNA levels of CDH11 in livers of BA patients with severe liver fibrosis significantly increased compared to BA patients with mild liver fibrosis (P< 0.01). Hepatic CDH11 mRNA levels were positively correlated with serum levels of γ-glutamyl transferase, total bilirubin, direct bilirubin and bile acid in children with BA (r= 0.26 ~ 0.37, all P< 0.05). Conclusions The mRNA levels of CDH11 were significantly increased in livers of BA patients compared to CC patients. The expression levels of CDH11 were associated with the progression of liver fibrosis and degree of liver injury in BA.