Background: Little information exists on malaria burden, artemisinin-based combination therapy (ACT) use, and malaria care provided to infants under six months of age. The perception that malaria may be rare in this age group has led to lack of clinical trials and evidence-based treatment guidelines. The objective of this study was to identify malaria parasitemia positivity rate (MPPR) among patients under six months, and practices and predictors of malaria diagnosis and treatment in this population. Methods: Cross-sectional data collected from October 2010 to September 2011 on 25,997 individual outpatients aged <6 months from 36 health facilities across Uganda were analysed. Findings: Malaria was suspected in 18,415 (70.8%) patients, of whom 7,785 (42.3%) were tested for malaria. Of those tested, the MPPR was 36.1%, with 63.9% testing negative, of which 1,545 (31.1%) were prescribed an antimalarial. Among children <5kgs, off-label prescription of ACT was high (104/285, 36.5%). Younger age (1-6 days, aOR=0.47, p=0.01; 7-31 days, aOR=0.43, p<0.001; and 1-2 months, aOR=0.61, p<0.001), pneumonia (aOR=0.78, p=0.01) or cough/cold (aOR=0.65, p<0.001) diagnosis, and fever (aOR=0.56, p=0.01) reduced the odds of receiving a malaria test. Fever (aOR=2.22, p<0.001), anemia diagnosis (aOR=3.51, p=0.01), consulting midwives (aOR=3.58, p=0.04) and other less skilled providers (aOR=4.75, p<0.001) relative to medical officers, consulting at hospitals (aOR=3.31, p=0.03), visiting health facilities in a medium-high malaria transmission area (aOR=2.20, p<0.001), and visiting during antimalarial (aOR=1.82, p=0.04) or antibiotic (aOR=2.23, p=0.04) shortages increased the odds of prescribing an antimalarial despite a negative malaria test result. Conclusions: We found high malaria suspicion but low testing rates in outpatient children aged <6 months. Among those tested, MPPR was high. Despite a negative malaria test result, many infants were prescribed antimalarials. Off-label ACT prescription was common in children weighing <5kgs. Evidence-based malaria guidelines for infants weighing <5 kilograms and aged <6 months are urgently needed.
