Introduction: Dengue and Chikungunya infections have similar clinical symptoms, which makes their clinical diagnosis complex. Moreover, both are transmitted by the same mosquito vectors, which results in virus co-circulation and co-infection. However, the outcome of these diseases differs: Chikungunya fever is rarely fatal but can have permanent and severe rheumatic and neurological sequelae, whereas dengue disease is potentially fatal. Thus, accurate diagnosis is critical. Objective: To compare presumptive diagnoses based on clinical findings with the differential diagnoses based on specific laboratory tests for each virus. Materials and methods: We performed specific virological and serological tests for both dengue and Chikungunya infections on eight acute-phase blood samples collected from pediatric patients with febrile syndrome. We used RT-PCR to detect dengue and Chikungunya virus, and IgM-capture ELISA to confirm infection by dengue virus. Results: Based on clinical findings, two patients were diagnosed as probable cases of dengue or Chikungunya, and two were diagnosed as probable cases of chikungunya. Four had no presumptive diagnosis of viral infection. Laboratory tests confirmed dengue infection in two patients, Chikungunya infection in two patients, and co-infection by the two viruses in the other four patients. Conclusion: Clinical findings were not sufficient to make a diagnosis in pediatric patients with febrile syndrome; specific laboratory tests were required to establish the etiologic agent of the disease.