SummaryWe report below an in vivo antimalarial efficacy study conducted in 2002 in Bundi Bugyo, a district of western Uganda housing a large displaced population. We tested sulfadoxine–pyrimethamine (SP), amodiaquine (AQ) and the combination chloroquine plus SP (CQ + SP). A total of 268 children with uncomplicated Plasmodium falciparum malaria were followed‐up for 28 days according to WHO recommendations, with PCR genotyping to distinguish late recrudescences from re‐infections. PCR‐adjusted failure proportions at day 28 were 37.0% (34/92, 95% CI 27.1–47.7) in the SP group, 20.6% (14/68, 95% CI 11.7–32.1) in the AQ group and 22.8% (18/79, 95% CI 14.1–33.6) in the CQ + SP group. Early failures were particularly frequent in the SP group (15.2%). Clearance of gametocytes was slower in the SP and CQ + SP groups than in the AQ group. This study suggests that, in Bundi Bugyo, CQ + SP (Uganda's first‐line regimen) will need to be replaced by a more efficacious regimen. Across Uganda, the deployment of SP containing combinations may not be a feasible long‐term strategy. For Bundi Bugyo, we recommend a combination of artesunate and AQ. Our study also confirms previous findings that resistance is considerably underestimated by 14‐day follow‐ups. Antimalarial policy decisions should therefore be based on 28‐day studies, with PCR adjustment to distinguish re‐infections.