We evaluated the in vivo responses to chloroquine (CQ), the first line antimalarial, and to sulfadoxine–pyrimethamine (SP), the most readily available and affordable alternative treatment, in children under 5 with acute uncomplicated Plasmodium falciparum malaria in seven sites of Democratic Republic of Congo (DRC) between May 2000 and November 2001, using the standard 14-day WHO protocol. In the CQ group, the overall treatment failure rate was 45.4% (95% CI: 40.1–50.8) of 350 infections successfully tested; in the SP group it was 7.5% (95% CI: 5.0–11.0) of 333 infections. Of 191 patients who had an adequate clinical response (ACR) in the CQ group, 127 (66.5%; range: 62.5–71.4) still had parasitaemia on day 14. In the SP group, only 21 (6.8%; range: 2.2–12.8) of 308 patients with an ACR were still parasitaemic on day 14. Using pooled data from three rural sites, haematological recovery was better in the SP group (mean of haematocrit difference between days 14 and 0 among anaemic children: 4.7 vs. 3.2; P < 0.01, Wilcoxon test). These findings suggest that CQ is no longer effective in DRC and that SP may be a good alternative for its replacement as first line antimalarial treatment. The Ministry of Health (MOH) therefore now recommends SP as the first line antimalarial drug in DRC, as an interim step, 18 months after launching the first study. Additional studies are needed to select alternative therapies that might replace SP or improve its efficacy, should it prove ineffective in the future.