Background:Sickle cell disease (SCD) contributes substantially to childhood mortality in sub-Saharan Africa. In the Republic of Uganda, the number of annual SCD births and the geographical distribution of the disease burden are unknown. A partnership between the Uganda Ministry of Health, Makerere University College of Health Sciences, and Cincinnati Childrenâs Hospital Medical Center was established to design and conduct the Uganda Sickle Surveillance Study.Objective: To describe the current prevalence and distribution of SCT and SCD in Uganda. The goals were to establish a partnership between academia and government, build local sickle cell laboratory capacity and determine the feasibility of testing a high-volume of samples for SCD, and create an accurate geospatial map of the SCD burden across Uganda.Methods: A Sickle Cell Laboratory was constructed and outfitted, and local personnel were recruited and trained. Hemoglobin electrophoresis was performed by isoelectric focusing on dried blood spots already collected in the Ministry of Healthâs Early Infant Diagnosis Program from HIV-exposed children over a one-year period, to identify and quantify the presence of sickle cell trait (SCT), SCD, and other hemoglobin variants.Results: A total of 99,243 dried blood spots were tested between February 2014 and March 2015, with 97,631 results successfully obtained. The national prevalence of SCT was 13.3%, ranging from 4.6% in the South Western region to 19.8% in the East Central region, and the SCD prevalence was 0.7%, ranging from 0.2% in the South Western region to 1.5% in the East Central region. SCT was detected in all districts, with the highest prevalence being 23.9% in Alebtong district. Analysis by region revealed that the observed SCT prevalence positively correlated with published malaria prevalence. SCD was less common in children older than 12 months and those who were HIV-positive, consistent with early mortality and co-morbidity.Conclusions: A successful North-South partnership joined academia and government to design and conduct an integrated national surveillance study, and to build local sickle cell laboratory capacity through training and program monitoring and evaluation. These successful strategies have positioned the Ministry of Health to begin to address the countryâs high disease burden, and will motivate and prioritize efforts for improving the management of SCD in Uganda.