Malaria is one of the most important infectious diseases worldwide. New therapies are needed, and it is generally agreed that combination therapy for uncomplicated malaria offers the best opportunity for effective therapy and for the prevention of selection of resistant parasites. Phase I of this study will be a randomized, single-blinded longitudinal clinical trial, comparing the efficacies of different combination antimalarial regimens for the treatment of uncomplicated malaria in a cohort of Ugandan children. The clinical study will be linked to an epidemiological survey and molecular analyses of parasite and human genetic polymorphisms. The aims of the study will be to: compare safety, tolerability, and efficacy of combination antimalarial therapies using a longitudinal design; follow plasmodial genetic polymorphisms as longitudinal markers of antimalarial drug resistance; and evaluate the roles of host genetic polymorphisms in antimalarial drug resistance and the incidence of clinical malaria. The clinical study will recruit participants from a defined and mapped source population in the Mulago III Parish, Kawempe District in Kampala, Uganda; conduct a survey of epidemiological factors on participants; and follow clinical care and outcomes over an extended period of time. Molecular analyses of parasite and human genetic polymorphisms will evaluate the impact of parasite mutations on treatment efficacy, the effects of repeated treatments on selection for resistance-mediating genotypes, and the impact of host polymorphisms on the incidence of malaria and responses to therapy. Phase I will include a random sample of 600 Ugandan children between the ages of 1-10 years. Participants will be followed for 3 years for all routine medical care in the study clinic at Mulago Hospital. Children presenting to the study clinic with a new episode of fever will undergo standard evaluation (history, physical examination and Giemsa-stained blood smear) for the diagnosis of malaria. Participants will be randomized to one of three combination treatment regimens at the time of their first diagnosis of uncomplicated malaria. Subsequent episodes of uncomplicated malaria will be treated with each participant's assigned treatment regimen. Clinical treatment failures occurring within 14 days of diagnosis and all episodes of complicated malaria will be treated with quinine, the standard therapy for malaria after treatment failure in Uganda. Routine home visits will be made for participants not seen in the clinic after any consecutive 30-day period. Routine home visits, made every 90 days, will include review of study protocol with the participants, assessment for any outside medical care, a focused history and physical examination and routine laboratory testing. Phase II will be a randomized, open-label, longitudinal clinical trial, comparing two combination antimalarial regimens. Following the first year of follow up, recruitment will be re-opened for children belonging to the same households previously recruited to the study, for children not previously enrolled ages 1-10 years. At this time, all participants will receive an insecticide treated bed net and phase II follow up will begin. All other aspects of subject evaluation, management, and follow-up will be the same as in Phase I, except that researchers will discontinue 30 day finger sticks (subjects will still be visited if they have not been seen in the clinic for 30 days, but finger sticks for blood smears and filter paper will only be performed during clinic evaluations, when clinically indicated or if the patient has not been evaluated in the clinic over a 90 day period). The primary outcome and endpoint (power calculations are based only on this endpoint) for this study will be treatment incidence density (treatments per time at risk) for each treatment arm. Secondary outcomes include drug efficacy and safety and tolerability. Protocol 05-0110 is a sub study of this protocol.