This study explored the use of participatory epidemiology (PE) to estimate the annual incidences of human diseases in Karamoja, Uganda, with emphasis on diseases associated with water. Adapted PE methods were used successfully to estimate disease incidences in young children and adults, and revealed a rich knowledge on the clinical signs and causes of diseases. The report concludes that PE could be useful for overcoming some of the spatial limitations of the health surveillance system in Karamoja, and the temporal limitations of bi-annual food security and nutrition assessments.