Background: Mortality among children under 5 years is an important health indicator. Therefore, determining the most common causes and manner of death according to the postmortem data is necessary for designing intervention programs to reduce mortality. Objectives: This study aimed to evaluate the causes and manner of death in children aged under 5 years old in Tehran, Iran using autopsy findings. Methods: This descriptive cross-sectional study was conducted on the data of all deaths among children aged under 5 years who were referred to the Legal Medicine Organization of Tehran, Iran, during January 2009-December 2019. The data were collected using the checklists of demographic characteristics, autopsy, toxicological findings, pathological findings, hospital records, and judicial documents, which were then analyzed. Results: Among 1750 children aged under 5 years old included in this study, 898 (51.3%) cases were male, and 997 (56.9%) were hospitalized. Most of the mortality cases occurred about two months after birth. The most common causes of death were found as congenital cardiovascular anomalies (14.7%), pneumonia (11.7%), and preterm labor (11%). Moreover, natural death (77.7%), accidental death (17.7%), homicide (2.7%), and unknown death (2%) were the major manners of death in these children. Conclusions: Postmortem examination to determine the causes of unnatural death could help clinicians and policymakers to propose a suitable intervention for reducing the mortality rate in children under 5 years.