There is a paucity of primary data to understand the overall pattern of disease and injuries as well as related health-service utilization in resource-poor countries in Africa. To generate reliable and robust data describing the pattern of emergency presentations attributable to communicable disease (CD), non-communicable disease (NCD) and injuries in three different regions of Mozambique. We undertook a pragmatic, prospective, multicentre surveillance study of individuals (all ages) presenting to the emergency departments of three hospitals in Southern (Maputo), Central (Beira) and Northern (Nampula) Mozambique. During 24-hour surveillance in the seasonally distinct months of April and October 2016/2017, we recorded data on 7,809 participants randomly selected from 39,124 emergency presentations to the three participating hospitals. Applying a pragmatic surveillance protocol, data were prospectively collected on the demography, clinical history, medical profile and treatment of study participants.