Quality of Routine Malaria Surveillance Data in Botswana’s Highest-Burden Districts, 2023–2025

High-quality malaria surveillance is essential for elimination.This study assessed routine malaria surveillance data quality in Botswana's highest-burden districts against WHO-recommended malaria elimination data-quality indicators and examined geographic and temporal variation during 2023-2025.A retrospective data-quality assessment used national Case-Based Surveillance (CBS) records and Integrated Disease Surveillance and Response (IDSR) aggregate counts.Districts were selected using a Pareto approach.Completeness, timeliness, internal consistency and CBS-IDSR agreement were assessed separately.Indicator proportions were summarized with 95% confidence intervals; geographic and annual differences were assessed using Pearson chisquare tests and multivariable logistic regression.The CBS dataset contained 3,393 records with valid analysis years.Okavango, Ngamiland and Chobe contributed 2,729 (80.4%) and formed the primary analytic population.Overall core-variable completeness was 79.5% (2,169/2,729), documented case investigation was 40.9% (1,117/2,729), notification within the day-level 24-hour approximation was 92.5% (2,409/2,603), investigation within 3 days among investigated cases was 58.0% (648/1,117), and internal consistency among evaluable records was 92.7% (825/890).Aggregate CBS-IDSR count agreement across the three districts was 95.7% (2,612 IDSR versus 2,729 CBS cases).Geographic differences were significant for all five case-level indicators (p < 0.001).Core completeness, documented investigation and investigation timeliness varied significantly by year, whereas notification timeliness (p = 0.640) and internal consistency (p = 0.311) did not vary significantly by year.Surveillance performance was heterogeneous across data-quality dimensions, districts and years.Timely notification and aggregate CBS-IDSR agreement were comparatively strong, whereas case-investigation documentation and timeliness remained important weaknesses requiring targeted surveillance strengthening.