Improper diagnosis and management of febrile patients results in the persistence of malaria and other conditions with similar symptoms. The algorithm established here with Rapid Diagnostic Tests (RDTs) will help in the follow-up and treatment of fever patients according to the guidelines on Integrated Management of Childhood Illness (IMCI). This study aimed at determining the causes of fever in children and at valorizing the use of RDTs for the diagnosis of febrile diseases. Fifty children with fever, aged between 0 and 5 years, were recruited in a cross-sectional study at the Ekounou Baptist Clinic in Yaounde. RDTs were used to assess for the four common causes of febrile illness in the area. Microscopy was done and the Plasmodium species were confirmed by nested Polymerase Chain Reaction (PCR). Of the 50 febrile children, none was rubella seropositive, while 8% had malaria, 22% had toxoplasmosis infection, 8% had Salmonella typhi, 14% had a malaria-typhoid fever co-infection, 4% had a malaria-toxoplasmosis co-infection, 6% had a malaria-toxoplasmosis-typhoid fever coinfection, and 38% were negative for all the suspected common causes of fever in the health district. The overall frequencies of occurrence attributed 32% to malaria, 32% to toxoplasmosis and 28% to typhoid fever. Among all the positive malaria cases (n=16 (32%)) Plasmodium falciparum, Plasmodium malariae and Plasmodium ovale were identified by nested PCR. Malaria RDT results agreed significantly with the microscopy (kappa=0.81; p<0.0001) and PCR (kappa=0.84; p<0.0001) results; and the microscopy results also concurred significantly with the PCR results (kappa=0.77; p<0.0001). Malaria was not the exclusive cause of fever. Toxoplasmosis was found to occur in the same proportion as malaria (32%) in the study population. S. typhi was the third most important infection. Therefore RDTs are appropriate tools for the management of childhood febrile diseases.