Many countries in Africa, including Sierra Leone, have adopted artemisinin-based combination therapy as first-line therapy for treatment of patients with malaria. Because laboratory testing is often unavailable in rural areas, the cost-benefit and viability of this approach may depend on accurately diagnosing malaria by using clinical criteria. We assessed the accuracy of syndromic diagnosis for malaria in three peripheral health units in rural Sierra Leone and determined factors that were associated with an accurate malaria diagnosis. Of 175 children diagnosed with malaria on syndromic grounds, 143 (82%) were confirmed by the Paracheck-Pf test. In a multivariate analysis, splenomegaly (P = 0.04) was the only clinical sign significantly associated with laboratory-confirmed malaria, and sleeping under a bed net was protective (P = 0.05). Our findings show that clinical malaria is diagnosed relatively accurately in rural Sierra Leone. Incorporating bed net use and splenomegaly into the national Integrated Management of Childhood Illness guidelines for evaluation of fever may further enhance diagnostic accuracy for malaria.