<h3>Background and aims</h3> Neonatal cholestasis is caused by either biliary atresia or intrahepatic cholestasis. Congenital combined pituitary hormone deficiency (CPHD) is a rare disease and a recognised cause of intrahepatic cholestasis. It is important to differentiate cholestasis due to this entity from cholestasis due to biliary atresia, since both diseases can cause jaundice at about 1 month of age. However, doing so in a timely fashion remains a diagnostic dilemma. This retrospective study was performed to clarify differences between cholestasis due to congenital CPHD and cholestasis due to biliary atresia. <h3>Methods</h3> From 2004 to 2010, 4 infants (2 boys and 2 girls) with cholestasis due to congenital CPHD were admitted to Nagoya City University Hospital. Head magnetic resonance imaging of the 4 infants revealed an invisible pituitary stalk; 3 of these 4 infants had an ectopic posterior pituitary. Liver biopsy was performed in 3 of the 4 infants, and histological findings included giant cell hepatitis. Findings from these 4 infants were then compared with those from55 infants treated in our hospital for cholestasis due to biliary atresia. <h3>Results</h3> The results showed a significant difference in mean gamma-glutamyl transpeptidase levels between the two groups of infants (115.0 IU/l vs. 553.0 IU/l, respectively). <h3>Conclusions</h3> The gamma-glutamyl transpeptidase level was found to be useful for distinguishing congenital CPHD from biliary atresia as the cause of cholestasis. The diagnosis of hypopituitarism should always be considered in infants with unexplained neonatal hepatitis.