The war in northern Uganda has had a debilitating effect on the mental health of children and adolescents in the population. This study measures the prevalence and considers the aetiology of psychological distress in war affected adolescents 4 years after the end of the conflict. This is a cross-sectional study of 205 adolescents, aged 12–19, from a boarding primary school in Gulu, northern Uganda. Four years after the end of the war, 57% of the students were still found to have clinically significant levels of post-traumatic stress symptoms using a similar cut-off score to previous studies among the same population. Both components of traumatic exposure: the number of types of traumatic event experienced; and whether the adolescent was abducted were significantly associated with psychological distress. There was a strong correlation between post-traumatic stress symptoms and internalising symptoms. War-affected adolescents may continue to suffer from significant psychological stress in the years following the cessation of conflict. Multiple exposure to a number of different types of traumatic event may directly increase the likelihood of psychological distress especially for those exposed to the most extreme violence. The feasibility of employing a locally developed and validated screening instrument is demonstrated.