Objectives: To compare the incidence of traumatic events and its association with symptoms of post-traumatic stress disorder in three population groups in northern Uganda and southern Sudan. Methods: Household and individual level data collected through a single-round cross-sectional demographic survey. Setting: The sub-counties of Yivu, Odupi and Midia in the northern Ugandan district of Arua and of Otogo in Yei River district in southern Sudan. Participants: Residents of these Ugandan and Sudanese sub-counties were categorized on the basis of citizenship and refugee status (i.e. as Ugandan nationals, Sudanese nationals or Sudanese refugees). The random sample population consisted of 3,323 adults (mean age: 30 years; 75% female) from 1,831 national and refugee households. Results: Sudanese refugees reported the highest number of violent events experienced or witnessed ever and in the past one year . Witnessing of traumatic events, ever and in the past year , significantly predicted PTSD in surveyed population. Sex, age, education and occupation were also significantly associated with the development of PTSD symptoms. The population prevalence of PTSD was estimated to be 48% for Sudanese stayees, 46% for Sudanese refugees and 18% for Ugandan nationals. Conclusions: Symptoms of PTSD in war-affected Sudanese populations can be partly explained by traumatic event exposures. The high prevalence of violence and symptoms of PTSD in refugee populations highlight the need for better protection and security in refugee settlements. Humanitarian agencies must consider the provision of mental health services for populations affected by war and forced migration.