Background: Liver fibrosis is a hallmark determinant of morbidity in biliary atresia (BA) even in success- fully operated cases. Responsible factors for this rapid progression of fibrosis are not completely defined. Aberrant expression of the transcription factor SOX9 and hepatic progenitor cells (HPCs) proliferation have roles in fibrogenesis in cholestatic disorders. However, they were not investigated sufficiently in BA. We aimed to delineate the relation of SOX9 and HPCs to fibrosis and its progression in BA.Methods: Forty-eight patients with BA who underwent an initial diagnostic liver biopsy (LB) and conse- quent intraoperative LB were recruited and compared to 28 cases with non-BA cholestasis that had an LB in their diagnostic workup. Liver fibrosis, tissue SOX9 and HPC expressions were studied in both BA and non-BA-cholestasis cases. Liver fibrosis, SOX9, and HPCs\' dynamic changes in BA cases were assessed. Relation of fibrosis and its progression to SOX9 and HPCs in BA was assessed. Results: SOX9 and HPCs in ductular reaction (DR) form were expressed in 100％ of BA and their grades increased significantly in the second biopsy. The rapidly progressive fibrosis in BA, represented by fi- brosis grade of the intraoperative LB, correlated significantly to SOX9-DR and HPC-DR at the diagnostic ( r = 0.420, P = 0.003 and r = 0.405, P = 0.004, respectively) and the intraoperative ( r = 0.460, P = 0.001 and r = 0.467, P = 0.001, respectively) biopsy. On the other hand, fibrosis, SOX9-DR, and HPC-DR were significantly lower in non-BA cases at a comparable age ( P < 0.001, P = 0.006, and P = 0.014, respec- tively).Conclusions: Fibrosis in BA is rapidly progressive within a short time and is significantly correlated to SOX9 and HPCs. Assessment of targeting SOX9 and HPCs on fibrosis progression is warranted.