The implementation of programmes to control neglected tropical diseases (NTDs) requires up-to-date information on the prevalence and distribution of each NTD. This study evaluated the performance of reagent strip testing for haematuria to diagnose Schistosoma haematobium infection among school-aged children in the context of a rapid mapping survey in Southern Sudan. The reagent strips were highly sensitive (97.8%) but only moderately specific (58.8%). The proportion of false positive diagnoses was significantly higher among girls than boys, especially among girls aged 5-10 years. These findings suggest that reagent strips alone are not sufficient for rapid mapping surveys. A two-step approach is thus recommended whereby haematuria-positive urine samples are subsequently examined using urine filtration.