Abstract Background Lymphatic vessels (LVs) are crucial in immune reactions and serve as principal conduits for immune cells. However, till date, no study has analyzed the morphological changes in the LVs of patients with biliary atresia (BA). In this study, we aimed to determine the morphological changes in the LVs of the liver in patients with BA, elucidate their correlation with the morphology of the portal vein (PV) branches, and discuss their etiopathogenetic significance. Methods Morphometric analyses of liver biopsy specimens from patients treated between 1986 and 2016 were performed. The parameters measured were as follows: the whole liver area of the specimen, the fibrotic area, the number of LVs, LVs without patent lumen (designated as Ly0) and PV branches, and the diameters of the LVs with patent lumen and PVs. Results The number of LVs, Ly0, and PV branches per unit area of the whole liver specimen was significantly higher in patients with BA than in control participants with liver disease and those with normal livers. However, no correlation was observed between the fibrotic area and the average diameter of LVs or PVs, as well as between the fibrotic area and the number of LVs or PV branches. Furthermore, no correlation was observed between the total number of LVs and the number of PV branches. Conclusions The present study showed a significant increase in the total LVs and Ly0, characterized by a high Ly0 to total LVs ratio, suggesting that lymphangiogenesis occurs in the liver of patients with BA.