Background: Nodding syndrome, a disabling epidemic epileptic encephalopathy, has affected an estimated 1,834 children in northern Uganda, with reports of as many as 3,000. Etiology is unknown and children are being treated symptomatically but inconsistently with anti-epileptic drugs. Design: This qualitative study comprised 10 semi-structured interviews with caregivers of affected children and five focus group discussions with 23 participants; relatives, teachers, and religious leaders. Data collection and participant observation were carried out from July to September 2012 in Kitgum and Pader districts. The material was coded through inductive thematic analysis. Results: Nodding syndrome has brought signs of discrimination in school admission procedures, founded in a fear of transmission. The suffering and loss caused by nodding syndrome is collective, and participants felt that nodding syndrome was viewed as a threat to the Acholi only, and that interventions had therefore been delayed. Multiple theories of causation exist, most commonly that the disease is caused by chemicals from bombs or that food aid distributed in IDP camps had expired or been poisoned.A feeling of uncertainty was present in all focus group discussions, fueled by the fact that results of investigations were not being shared with the communities. It was especially agonizing that CDC results had been given to the Ugandan government in 2010 but not to the public. The definitive fear is that the disease will be the end of the Acholi. Conclusions: This study provided insight into the perceptions of communities affected by an unknown emerging disease. Families of affected children are grieving not only their child's illness; it is a loss of social value and of lineage. The loss and suffering involved with nodding syndrome should be seen in the context of the wider suffering of a society disrupted by violent conflict. The memory of war is omnipresent and is also how nodding syndrome is understood.