Background: The first duty of any government is to ensure the health of its children and neonates. Today's countries are classified as declining mortality in this group. To increase neonatal survival rate, classified causes of newborn mortality are the core strategy and policies. This study was aimed to determine the classification of causes of neonatal death in Iran. Methods: Neonatal mortality refers to deaths of young children. It is measured by the neonatal mortality rate (NMR), which is the number of deaths of neonates per 1000 live births. This study was used data from 11693 neonatal deaths (from 22 weeks gestational age to neonatal death less than 30 days), in Iran's hospitals in 2012 that registered in the perinatal mortality surveillance system (hospital-based system). Demographic characteristics and other factors associated with neonatal death were investigated. To aid in cause of death analysis, burden of disease analysis, and comparative risk assessment we classified the causes of death according to international statistical classification of diseases version 10 (ICD 10), divided into three cause mortality strata. Results: Results showed the most common cause of neonatal mortality was "certain conditions originating in the perinatal period" (77.92%) with the highest incidence of "disorders related to length of gestation and fetal growth" (37.7%) in this group. Also it shows that 20.82% of deaths caused by "congenital malformations, deformations and chromosomal abnormalities" and 1.26% cases had occurred as a result of "accidents and injuries". The greatest cause of death in the neonates with weight over one thousand grams was "certain conditions originating in the perinatal period" (71.29%), with the highest percentage in the disorders related to "length of gestation and fetal growth" (29.65%). Conclusion: According to this study the "certain conditions originating in the perinatal period" special "disorders related to length of gestation and fetal growth" was the main cause of neonatal mortality. Also "congenital malformations, deformations and chromosomal abnormalities" was the second cause of neonatal mortality.