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BackgroundCivil wars in the Great Lakes region resulted in massive displacement of people to neighboring countries including Uganda, with associated humanitarian emergencies. Appropriate disease surveillance enables timely detection and response to outbreaks. We describe evaluation of the public health surveillance system in refugee settlements in Uganda and document lessons learnt.MethodsWe conducted a cross-sectional survey using the US CDC Updated Guidelines for Evaluating Public Health Surveillance Systems in four refugee settlements in Uganda i.e., Bidibidi, Adjumani, Kiryandongo and Rhino Camp. Using semi-structured questionnaires, key informant and focus group discussion guides, we interviewed health facility in-charges, key personnel and village health teams from 4 districts, 53 health facilities and 112 villages.ResultsAll health facilities assessed had key surveillance staff; 60% were trained on IDSR and most village health teams were trained on disease surveillance. Case detection was at 55%; facilities lacked standard case definitions (SCDs) and were using parallel Implementing Partner (IP) driven reporting system. Recording was at 79% and reporting was at 81%. Data analysis and interpretation was at 49%. Confirmation of outbreaks and events was at 76%. Preparedness was at 72% and response was at 34%. Feedback was at 82%. Recording, reporting, preparedness, feedback and confirmation of outbreaks and events were highly achieved, and capacity to evaluate and improve the system was moderately achieved. There were low scores in capacity to detect, respond and analyse data.ConclusionPublic health surveillance system had high sensitivity, timeliness and predictive value positive. It was simple, acceptable with fair data quality attributes. It was less flexible, less stable with low representativeness. The system had good recording, reporting, preparedness, feedback and confirmation of outbreaks and events. The capacity for detection, response and data analysis and interpretation was low. Lessons learnt were: IPs offer tremendous support to surveillance; training of surveillance staff on IDSR maintains effective surveillance functions; supplies of tools, personnel etc. should be planned and executed; functionalization of district teams ensures achievement of surveillance functions and attributes; regular support supervision of health facilities necessary; harmonization of reporting improves surveillance functions and attributes; appropriation of funds to districts to support refugee settlements is complementary.