Background: There is little information on the effectiveness of modern compared to traditional malaria treatment from the rural areas of Africa. Methods: Follow-up of 402 episodes of clinical malaria among pre-school children in Nouna Health District, northwestern Burkina Faso. The exposure of interest was the type of treatment (chloroquine versus traditional); the outcome was clinical response to treatment. Results: Out of the 402 observed malaria episodes, 87% were treated with chloroquine and 13% with traditional remedies. Overall, community effectiveness was 67% with chloroquine and 54% with traditional treatment. Chloroquine effectiveness was associated with age and ethnicity. An additional interview survey demonstrated wide variations in the dosages of chloroquine given to young children in this community. Conclusions: The effectiveness of chloroquine, when used within the community, was significantly lower in this study than its known efficacy in the study area. This concerns, in particular, the very young children. These findings demonstrate the need for better education of parents about correct dosage of first-line malaria drugs, and for particular attention in the treatment of very young children.