Cystic biliary atresia (CBA), a rare cystic expansion of atretic extrahepatic bile ducts in young infants, overlaps in age at presentation and imaging features with early choledochal cysts (CC). Treatment and prognosis differ; histologic differences are unsettled. We compared 10 patients with CBA, 1975 to 2015, to an age-similar cohort of 13 infants, and to older patients who had surgery for CC. Operative details, imaging, and clinical courses were correlated to pathologic specimens. Immunostains for smooth muscle actin and myosin heavy chain were used to evaluate cyst walls and atretic segments. CBA cysts typically lacked epithelium and inflammation; cyst walls had an inner, dense cicatricial layer associated with myofibroblastic (MF) hyperplasia that often delaminated producing a grossly visible inner cyst wall. Seven proximal biliary remnants in CBA featured circumferential peribiliary MF hyperplasia/fibrosis with little or no inflammation, similar to isolated BA. Extrahepatic atresia was usually both proximal and distal to the cyst. Features in 10/13 CC from infants and 8/8 CC in older patients had mostly preserved uninjured epithelium and no subepithelial cicatrix. Mural smooth muscle (absent in CBA) was present to some extent in CC at all ages. Unexpectedly, focal MF hyperplasia and laminar sclerosis was present in a few CC in infants, resembling CBA. CBA and infant CC are distinct histologic entities that occasionally overlap. CBA bile duct injury mimics non-CBA. Cystification is an aberrant manifestation of stromal proliferation in BA. The current management approach assuming CBA and CC in infants are 2 separate disease processes is supported but caution is advised.