Zellweger syndrome (ZS) is a peroxisomal disorder with a multiple congenital anomalies, characterized by stereotypical facies, profound hypotonia, organ involvement including cerebral, retinal, hepatic, and renal. Herein, a 3-month-old female with ZS is presented who was referred because of increased liver enzymes (subclinical hepatitis), which was detected in work-up of her neck cyst, severe hypotonia, and abnormal facies. An increased concentration of very long chain fatty acid in lipid profile was detected. ZS should be considered in the list of differential diagnosis in infants with stereotypical phenotype, neurodevelopmental delay, and severe hypotonia in association with liver and other organs involvement.