Objective To examine the accuracy of mortality statistics in Palestine, to identify gaps and to provide evidence-based recommendations to improve mortality statistics in Palestine. Study design and setting A retrospective death registry-based study that examined a stratified random sample of death notification forms (DNFs) of patients who died in hospitals in Palestine was reported in 2012. We randomly selected 600 deceased from the Cause of Death Registry: 400 from the West Bank and 200 from the Gaza Strip. Analysis was based on the randomly selected deaths that we were able to retrieve the medical records for; 371 deaths in the West Bank and 199 deaths in the Gaza Strip. Results Data in the Palestinian Health Information Centre (PHIC) registry had a low degree of accuracy: less than half of the underlying causes stated the correct cause of death. In general, deaths due to malignant neoplasms were more accurately reported on DNFs than other causes of death, and metabolic diseases (including diabetes) were the most problematic. Issues with coding and classification at the PHIC were most apparent for perinatal conditions and congenital anomalies. Conclusion Procedures for coding and classification at the PHIC deviate considerably from the international norms defined in the International Statistical Classification of Diseases and Related Health Problems (ICD) and account to a considerable extent for the discrepancies between the cause of death determined on the medical data on the death extracted from the deceased patient's hospital records and the cause of death coded by the PHIC. We recommend the introduction of international coding software for coding and classification, and a review to improve data handling in hospitals, especially those with electronic patient records.