【Objective】To investigate the significance of liver biopsy in differential diagnosis and prognosis of congenital biliary atresia（CBA）and infant hepatitis syndrome（IHS）.【Methods】Totally 77 children with congenital biliary atresia and 48 infants with hepatitis syndrome treated in Guangdong Women and Children Hospital from December 2012 to December 2016 were examined by liver biopsy and follow-up. Combined with immunohistochemistry and PAS staining，reticular fiber staining，Masson staining techniques，we make comparative analysis of both histopathological fea? tures and prognosis.【Results】The liver fibrosis grade，hepatic lobule inflammation activity staging，the degree of bile duct hyperplasia and the prognosis of CBA and IHS infants were statistically significant（P<0.05）. S2-S3-based liver fi? brosis grading in infants with CBA，mainly in G2-G3 hepatic lobule inflammation staging，bile duct hyperplasia signifi? cantly；IHS infants with liver fibrosis grading as S0-S1，liver Slice inflammatory activity stage to G1-G2-based. The prog? nosis of infants with CBA was significantly worse than IHS，and the difference was statistically significant（P<0.05）. 【Conclusion】The early liver biopsy of infants with congenital biliary atresia and infant hepatitis syndrome，combined with immunohistochemistry and PAS staining，reticular fiber staining，Masson staining techniques has important clinical significance to the differential diagnosis and prognosis of both.