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Background: The aim of this study was to establish the prevalence of posttraumatic stress disorder (PTSD) and depression among Rwandese and Somali refugees resident in a Ugandan refugee settlement, as a measure of the mental health consequences of armed conflict, as well as to inform a subsequent mental health outreach program. The study population comprised a sample from 14400 (n = 519 Somali and n = 906 Rwandese) refugees resident in Nakivale refugee settlement in South Western Uganda during the year 2003. Methods: The Posttraumatic Diagnostic Scale (PDS) and the Hopkins Symptom Checklist 25 were used to screen for posttraumatic stress disorder and depression. Results: Thirty two percent of the Rwandese and 48.1% of the Somali refugees were found to suffer from PTSD. The Somalis refugees had a mean of 11.95 (SD = 6.17) separate traumatic event types while the Rwandese had 8.86 (SD = 5.05). The Somalis scored a mean sum score of 21.17 (SD = 16.19) on the PDS while the Rwandese had a mean sum score of 10.05 (SD = 9.7). Conclusion: Mental health consequences of conflict remain long after the events are over, and therefore mental health intervention is as urgent for post-conflict migrant populations as physical health and other emergency interventions. A mental health outreach program was initiated based on this study.