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Background: Neonatal Cholestasis is an important infant__AWT_QUOTE__s diseases of liver and biliary, they are wide range of situation including; idiopathic neonatal hepatitis, extrahepatic biliary tract atresia, Choledochal cysts and infectious diseases. Lack of early diagnosis of the disease can be followed by irreparably complications. The aim of this study was determination the histopathological causes of neonatal Cholestasis in Shahid Sadoughi- Yazd hospital during 2006-2012. Methods: This study was a retrospective study; that performed in census method among 52 files have been archived in the pathology section Shahid Sadoughi- Yazd hospital regarding neonatal Cholestasis, during 2006-2012.For data collection includes; demographic, clinical and pathological was used a checklist. Data collected were analyzed by spss-18 with using descriptive statistics and chi-square test in a=0.05. Findings: 40.4% female and 59.6% percent were male. Respectively frequency of Idiopathic Neonatal Hepatitis (INH) and Extra Hepatic Biliary Atresia (EHBA) (90.4%) were more than other causes. EHBA Patients were older. Males more than females suffered of EHBA. Hepatomegaly in EHBA Patients was more than INH Patients. In Hneonatal more than neonatal EHBA had clear stool symptom (P=0.017). Conclusion: INH and EHBA were the main causes of neonatal Cholestasis. Clinical symptoms aren__AWT_QUOTE__t proper differential diagnose regarding INH and EHBA. It is suggest to differential diagnose used of liver biopsy test.