Purpose: To evaluate the diagnostic validity of MR cholangiography as a second-line imaging tool following sonography in the evaluation of neonatal cholestasis, we compared MR cholangiography with $^{99m}Tc$ DISIDA scan. Materials and Methods: We retrospectively evaluated sonography, $^{99m}Tc$ DISIDA scan and MR cholangiography in twenty-two neonates and infants (age range, 23-103 days; mean age, 57 days) presenting with conjugated hyperbilirubinemia. Of the 22 patients, 15 were diagnosed as biliary atresia by operative cholangiography and liver biopsy and six as neonatal hepatitis by imaging finding and clinical data. Remaining one patient was diagnosed as neonatal hepatitis by operative cholangiography and liver biopsy. Two independent observers for each study were assigned to review the images of $^{99m}Tc$ DISIDA scan and MR cholangiography without giving the final diagnosis or other clinical data. Diagnostic accuracy and interobserver variability for each study were evaluated. Results: On $^{99m}Tc$ DISIDA scan, biliary atresia was mistaken for neonatal hepatitis in eight patients and vice versa in four patients. On MR cholangiography, it was mistaken biliary atresia as neonatal hepatitis and vice versa in each two patients. Sensitivity, specificity, accuracy, positive and negative predictive values of $^{99m}Tc$ DISIDA scan were 48%, 47%, 48%, 66% and 30%, respectively, and those of MR cholangiography were 90%, 71%, 84%, 87% and 81%, respectively. Interobserver variabilities for $^{99m}Tc$ DISIDA scan and MR cholangiography were 0.62 and 0.85, respectively. Conclusion: In the evaluation of patients with neonatal cholestasis, it would be advisable to use MR cholangiography, having superior diagnostic accuracy to $^{99m}Tc$ DISIDA scan, as a second-line imaging tool following sonography.