Biliary atresia (BA) is a complex disorder for which the etiology is still far from clear. Newborn infants that develop BA may carry certain genetic defects, resulting in susceptibility to uncertain pathogens with characteristic pathogen-associated molecular patterns (PAMPs). The pathogens with their characteristic PAMPs in turn lead to activation of the innate immune system by triggering pattern recognition receptors on the immune cells. Toll-like receptors (TLRs) are the most recognized pattern recognition receptors and TLR signaling is the telltale sign of activation of innate immunity. The activation of TLR and the innate immune system in BA is demonstrated by the up-regulation of TLR7 and by the association of promoter polymorphism of CD14 with BA. The antimicrobial peptide hepcidin and MxA, a protein downstream of TLR7 signaling, which is also known as a highly specific marker for type I IFN signaling, are also found highly expressed in the early stage of BA. This review examines the known components of innate immunity involved in BA and outlines the potential role of the innate immune system, in cooperation with adaptive immunity, in the pathogenesis of BA.