Background:We aimed to evaluate the diagnostic value of anti-smooth muscle antibodies (ASMA) and two liver markers (gamma-glutamyl transpeptidase [GGT] and alkaline phosphatase [ALP]) for differentiating between patients with extrahepatic biliary atresia (EHBA) and idiopathic neonatal hepatitis (INH).Materials and Methods:During April 2010–2011, all infants at 2 weeks of age who were diagnosed with cholestasis and admitted to Children's Hospital of Tabriz were enrolled. Based on the results of physical examination, laboratory, imaging and pathological studies, neonates were divided into two groups (EHBA and INH). Receiver operating characteristics analysis was used to define sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy for ASMA, GGT and ALP.Results:Thirty neonates with cholestasis (18 with EHBA and 12 with INH) and mean age of 54.66 ± 25.86 days were enrolled. Total and direct bilirubin, serum glutamic oxaloacetic transaminase, serum glutamic pyruvic transaminase and ASMA titres were highly not significant (P > 0.05) in patients with INH. GGT (P = 0.008) and ALP (P = 0.01) had statistically significant differences that were higher in patients with EHBA. The sensitivity, specificity, PPV and NPV, accuracy, LR+ and LR− of SMA in differentiating cases with BA were 66.7%, 75%, 80% 60%, 70%, 2.68 and 0.44, respectively. For GGT, the values were 88.9%, 66.7%, 80%, 80%, 79.1%, 3.08 and 0.31, respectively. Finally, for ALP, the values were 77.8%, 75%, 82.4%, 69.2%, 80%, 2.66 and 0.24, respectively.Conclusion:Our study showed that ASMA may be a useful biomarker for differentiation of EHBA from INH. Further studies with larger samples are recommended for confirming the results of this study.