BACKGROUND: The signing of the Comprehensive Peace Agreement in January 2005 marked the end of the civil conflict in Sudan lasting over 20 years. The conflict was characterised by widespread violence and large-scale forced migration. Mental health is recognised as a key public health issue for conflict-affected populations. Studies revealed high levels of post-traumatic stress disorder (PTSD) amongst populations from Southern Sudan during the conflict. However, no studies have been conducted on mental health in post-war Southern Sudan. The objective of this study was to measure PTSD and depression in the population in the town of Juba in Southern Sudan; and to investigate the association ofdemographic, displacement, and past and recent trauma exposure variables, on the outcomes of PTSD and depression. METHODS: A cross-sectional, random cluster survey with a sample of 1242 adults (aged over 18 years) was conducted in November 2007 in the town of Juba, the capital of Southern Sudan. Levels of exposure to traumatic events and PTSD were measured using the Harvard Trauma Questionnaire (original version), and levels of depression measured using the Hopkins Symptom Checklist-25. Multivariate logistic regression was used to analyse the association ofdemographic, displacement and trauma exposure variables on the outcomes of PTSD and depression. Multivariate logistic regression was also conducted to investigate which demographic and displacement variables were associated with exposure to traumatic events. RESULTS: Over one third (36%) of respondents met symptom criteria for PTSD and half (50%) of respondents met symptom criteria for depression. The multivariate logistic regression analysis showed strong associations of gender, marital status, forced displacement, and trauma exposure with outcomes of PTSD and depression. Men, IDPs, and refugees and persons displaced more than once were all significantly more likely to have experienced eight or more traumatic events. CONCLUSION: This study provides evidence of high levels of mental distress in the population of Juba Town, and associated risk-factors. Comprehensive social and psychological assistance is urgently required in Juba.