Biliary atresia (BA) is an inflammatory cholangiopathy of unknown etiology. Maternal microchimerism has been identified in the livers of patients with BA. We analyzed the human leukocyte antigen (HLA) compatibility between 57 BA patient-mother pairs and 50 control-mother pairs. The HLA class I matching was significantly more frequent in BA pairs (odds ratio [OR]=2.46) than controls. Similar results were also found in child-to-mother HLA compatibility (OR=2.16). Our results indicate that patients with BA have an immunogenetic histocompatible relationship with their mothers, which may result in an increase in maternal microchimerism found in BA.