Burkina Faso has recently changed the antimalarial drug policy to artesunate/amodiaquine or artemether/lumefantrine as the first-line antimalarial drug and sulfadoxine/pyrimethamine for the intermittent preventive treatment in pregnant woman. Before the implementation of this new strategy we conducted an in vivo efficacy study with chloroquine or sulfadoxine/pyrimethamine for treatment of uncomplicated Plasmodium falciparum malaria in urban area of Burkina from September to December 2003. Chloroquine (25 mg/kg over 3 days) or sulfadoxine/pyrimethamine (25 mg/kg + 0.025 mg/kg single dose) was administered respectively to 137 and 125 children aged from 6 to 59 months old in a randomized, opened study. Follow up extended over 28 days using modified WHO protocol. After adjusting the results by PCR, treatment failures rates were 63.4% (83/131) and 13.8% (17/123) respectively for chloroquine and sulfadoxine/pyrimethamine. These results with other observations have justified the change of malaria therapy policy in Burkina Faso in 2005.