<p>Strong malaria surveillance is fundamental for program planning. Malaria ‘epidemics’ are detected by applying thresholds calculated using any of three WHO-recommended methods [the 75th percentile or mean+2 standard deviations (2SD) (for high-transmission areas), and cumulative sum (C-SUM) methods (for low-transmission areas)] to weekly surveillance data. The C-SUM method is not recommended for high-transmission areas due to its high sensitivity and potential for false alarms. In Uganda, districts can apply either the 75th percentile or mean+2 standard deviation methods. We evaluated the different threshold approaches to compare their epidemic-signaling outputs in Uganda.</p>