Civil wars in the Great Lakes region resulted in massive displacement of people to neighboring countries including Uganda. With associated disease epidemics related to this conflict, a disease surveillance system was established aiming for timely detection of diseases and rapid response to outbreaks. We describe the evaluation of and lessons learned from the public health surveillance system set up in refugee settlements in Uganda (Bidibidi, Adjumani, Kiryandongo and Rhino Camp). We found that it was functional with many performing attributes but with many remaining gaps. There is need for improvement to align surveillance systems in refugee settlements with the mainstream surveillance system in the country.