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The median age of cases and controls in years was 35 (IQR = 19) and 38 (IQR = 19) respectively. Variables that had a significant association with HIV-malaria co-infection were non-in-door residual spraying (adjusted odds ratio (AOR) = 4.91; 95% CI 4.03, 15.13), poor perception on the health risk of HIV-malaria co-infections (AOR = 4.11; 95% CI 1.28, 10.17), non-use of insecticidal treated bed nets (AOR = 6.21; 95%CI 2.74, 14.11), non-use of cotrimoxazole prophylaxis (AOR = 2.42; 95% CI 1.11, 5.28), and not received health education