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Objective To determine the spatial-temporal patterns of natural hazards and disasters in the Greater Horn of Africa, including climate and environmentally sensitive diseases, and compare the reporting consistencies across multiple open-access databases.Design Cross-sectional retrospective secondary analysis of natural hazard and disaster data.Setting Djibouti, Eritrea, Ethiopia, Kenya, Somalia, Sudan, South Sudan and Uganda.Data sources Primary data from Emergency Events Database (EM-DAT), and comparative data from ReliefWeb, WHO Disease Outbreak News (WHO-DON), FloodList and Global Unique Disaster Identifier Number (GLIDE).Results EM-DAT reported 228 natural hazards and disasters affecting 145.7 million people; highest numbers reported in Uganda (n=48), Kenya (n=46), Somalia (n=38) and Ethiopia (n=35); 175 geophysical, hydrological, meteorological and climatological hazards reported, including 118 floods, 26 droughts, 11 storms and 17 landslides; 46 epidemics reported, primarily bacterial (eg, cholera) or viral (eg, yellow fever, measles) diseases, with 20% preceded by a flood, drought or landslide within the previous 3 months. Reporting consistency and content varied considerably across the five databases.Conclusion Natural hazards and disasters affect millions of people. There is an urgent need to improve database connectedness to facilitate better monitoring and mapping, which can inform disease forecasting and decision tools to develop preparedness and intervention strategies.