Introduction: Neonatal Mortality in hospitalized patient is one of the major concerns globally. Despite of many initiatives, it is still a health challenge. In Afghanistan, neonatal mortality rate (NMR) is estimated as 45/1000 live births which is alarming and one of the highest rate in the world. This study aimed to identify the causes of mortality and its associated factors among neonates in French Medical Institute for Children, Kabul Afghanistan. Methodology: We conducted an analytical retrospective hospital based study to achieve the current study objectives. We extracted the records of 110 neonates who have died during hospitalization at FMIC due to somatic and/or organic diseases from January 2013 to December 2014. A structured checklist was developed to collect information for different variables. Data was analyzed with the help of Statistical Package for Social Sciences (SPSS) Version 19.0. Chi-square test of independence was run for association between predictors and outcome variables. The study is approved by Institutional Ethical Review Board of Ministry of Public Health. Results: Among all the causes, Septicemia was found to be the leading cause of neonatal mortality and 60% of the neonates had died due to this cause. Following Septicemia, Pneumonia was the next leading cause of neonatal deaths and around 21% of the participants had died due to this second leading cause of mortality. On the other hand, meningitis contributed 10.91% in neonatal deaths. Around 7.27% of the deaths were due to complication of prematurity i.e. respiratory distress syndrome. One of the complications of prematurity was necrotizing Entero colitis which leads to 5.45% neonatal deaths. Ten percent of neonatal mortality was due to birth asphyxia, 10.91% because of meconium aspiration ix syndrome, and only 1.82% deaths due to TGA with closing PDA which is cyanotic type of congenital heart diseases in our study. In addition, this study has also showed that mortality due to Septicemia was significantly associated with birth weight and gestational age. Our research was unable to explore the socioeconomic factors associated with mortality due to Pneumonia.Conclusion: Neonates are the high risk population in Afghanistan. This study has estimated proportions of neonatal mortality due to Septicemia and Pneumonia as 60% and 21% respectively. Immediate and long term actions are required to change the current situation and improve the overall neonatal health at home, facility and hospital levels. The recommendations have implications for ministry of public health to devise relevant and appropriate interventions and policies