Biliary atresia is an idiopathic neonatal cholestatic disease characterized by the destruction of both the intra- and extra-hepatic biliary ducts. There are two clinical manifestations of the disease: an embryonal subtype, which often presents at birth and is associated with congenital malformations, and a 'perinatal' subtype, which is probably an acquired disease due to unknown etiology. Over the last two decades, researchers have focused on activation of the cell-mediated immunity as the mechanism for biliary epithelial cell destruction for the latter subtype. A proposed trigger of this immune response is an initial viral infection, inducing biliary epithelial cells to become antigen-presenting cells and thus instigating immune-mediated destruction of the biliary tract. However, putative viruses have never been confirmed. More recently, a novel hypothesis - that maternal microchimerism may initiate a host immunologic response towards the bile duct epithelia - has been proposed. This paper discusses the etiology of biliary atresia in the context of the current research.