Objective. The diagnosis of biliary atresia (BA) can be challenging as its histopathologic features overlap with those of other pediatric cholestatic liver diseases. We aimed to study the diagnostic value of hepatic IFN-γ and CD68 immunostaining in the differentiation of BA from other causes of neonatal cholestasis. Methods. Hepatic IFN-γ and CD68 immunostaining were investigated in 69 patients divided according to the diagnosis into BA group (n= 34) and non-BA group (n= 35). The semi quantitative assessment included estimating the average of positive staining cells among inflammatory infiltrate in portal tracts of this liver biopsy. Results. The mean of hepatic CD68 and IFN-γ immunostaining in patients with BA was significantaly higher (41.2 ± 9.2 and 39.3 ± 12.6 respectively) than in cholestasis group (20.8 ± 15.2 and 21.5 ± 15.7 respectively). With cutoff values of 24 for CD68 and 22 for IFN-γ could differentiate between BA and cholestatic patients with sensitivity and specificity of 94.18% and 74.30% for CD68 and 89% and 73.14% for IFN-γ. Conclusion. Both IFN-γ and CD68 immunostaining of the liver had a diagnostic value in differentiation between BA and other neonatal cholestatic disorders and might be useful as an additional stain when investigating infants with neonatal cholestasis.