Objectives: This study reports frequency of different causes of infant cholestasis diagnosed by clinical and biochemical parameters as well as liver biopsy. Methods: Cholestasis persisting beyond two-weeks of age in 46 infants less than 6 months old was evaluated. A checklist including signs and symptoms, as well as laboratory, imaging and liver biopsy results was prepared. According to diagnosis, patients were classified into two groups: biliary atresia (BA) and non-biliary atresia (Non-BA) and results were compared between two groups. P value < 0.05 was considered significant. Results: Forty six infants (25 girls, 21 boys) with cholestasis and mean age of 65 ± 99 days were included in the study. Most of the infants (42%) were referred at the age of > 91 days. The most common symptoms and signs were jaundice in 100% followed by hepatomegaly (78%), splenomegaly (52%), acholic stool (35%) and dark urine (37%). There were no significant differences between the two groups for age, gender, onset of jaundice and organomegaly. Patients in BA group experienced more acholic stool, abnormal AST, ALT and bilirubin (P < 0.05). The most common underlying causes of liver disease in study group were BA (30.4%) and idiopathic neonatal hepatitis (INH) in 30.4% followed by metabolic disorders. Conclusions: Sixty one percent of infants with cholestasis in present study had BA and INH. A systemic approach is the key for rapid diagnosis to rule out BA and other treatable disorders for a better outcome.