OBJECTIVE Extrahepatic biliary atresia (EHBA) is one of the main causes of neonatal cholestasis. Its early diagnosis could increase the survival of the infants with early surgery. We evaluated the diagnostic accuracy of procalcitonin and apolipoprotein E (Apo-E) levels in infants with and without EHBA. METHODS This prospective study included 18 infants with EHBA and 15 infants with other causes of cholestasis. Blood samples were taken from each patient and different markers including procalcitonin and Apo-E levels were measured. ROC analysis was used to define sensitivity, specificity, positive and negative predictive value (PPV and NPV) for procalcitonin and Apo-E. Findings : There was a significantly positive correlation between Apo-E and SGOT (r=0.37, P=0.03), SGPT (r=0.38, P=0.02) and GGT (r=0.38, P=0.02), and an inverse correlation between procalcitonin and GGT (r=-0.45, P=0.01). Area under curve (AUC) for procalcitonin was 0.69 (P=0.05) with cut-point of 0.735 ng/ml. The sensitivity, specificity, PPV and NPV was 67%, 61%, 69% and 59%, respectively. AUC for Apo-E was 0.68 (P=0.06) for cut-point of 61.25 ng/ml with sensitivity, specificity, PPV and NPV of 67%, 67%, 71% and 67%, respectively. CONCLUSIONS Both PCT and Apo-E have relatively good accuracy in diagnosing EHBA cases; we could not rely on these markers for diagnosis of EHBA, however, combinations of these biomarkers with other markers and imaging tests could improve their accuracy and may help to achieve a rapid and accurate diagnosis of EHBA.