Aim of the study:To determine the hepatic interferon γ (IFN-γ) and tumor necrosis factor a (TNF-a) levels in infants with neonatal cholestasis (NC) and associated cytomegalovirus (CMV) infection. Material and methods: This study was conducted in 21 infants with NC over a period of 6 months from June 2017 to December 2017 to determine the hepatic IFN-γ and TNF-a levels in infants with NC and associated CMV infection. Results: IFN-γ levels were positive in 16 (80%), low positive in 3 (16%) and negative in 1 (5%) patients. High positive and positive TNF-a levels were seen in 9 (56.3%) patients with positive liver CMV PCR and low positive levels were seen in 7 (43.7%) patients with positive liver CMV PCR (odds ratio [OR] = 2.6). Positive IFN-γ was present in 13 (81.3%) patients with positive liver CMV PCR and low positive or negative IFN-γ was seen in 3 (18.7%) patients with positive liver CMV PCR (OR = 2.2). Six (60%) patients with positive or high positive TNF-a levels in liver tissue had biliary atresia (BA) whereas 7 (77.7%) with low positive TNF-a levels had non-BA neonatal hepatitis (OR = 5.25). Six (37.5%) patients with positive IFN-γ had BA whereas 2 (50%) patients with low positive or negative IFN-γ had BA (OR = 0.6). Conclusions: There is high prevalence of CMV in liver tissues in patients with NC and elevated TNF-a and IFN-γ levels are seen in these patients. Elevated TNF-a is also seen in patients with BA. The association of elevated TNF-a, BA and CMV infection needs to be evaluated further.