The objective of this study was to evaluate the impact of a new malaria protocol introduced in 2007 at Nyarugusu Refugee Camp. In accordance with this protocol, the delivery of a diagnostic test (rapid diagnostic test or microscopy) was made compulsory prior to the administration of antimalarial drugs (ACTs: artemisinin-based combination therapies). We collected camp clinic records on outpatient malaria diagnoses from 2004 through 2007 and compared the morbidity percentages attributed to malaria during these years, as well as the actual incidence of malaria in 2006 and 2007. Our analyses demonstrate that malaria accounted for 45.8% of all morbidity in 2004 (64,557 malaria cases out of 1,40,669 total morbidity), followed by corresponding figures of 47.8% for 2005 (94,389 malaria cases out of 1,97,400) and 47.9% for 2006 (60,760 malaria cases out of 1,26,754); however, the values dropped sharply to 22.8% in 2007 (20,136 malaria cases out of 88,254). We found a similar drastic drop in the incidence of malaria from an average of 182.415 cases/1000 inhabitants/month in 2006 to only 35.635 cases/1000 inhabitants/month in 2007. The results of our study suggest that because of the overlap of symptoms from malarial and non-malarial febrile illnesses, diagnosing malaria on clinical and epidemiological bases may lead to its overdiagnosis. This could result in both the overprescription of antimalarials and the underdiagnosis and inappropriate treatment of non-malarial febrile processes. The use of affordable and available tests can increase the accuracy of malaria diagnoses, so that only real malaria cases would be treated as such. This would help curb the uncontrolled administration of antimalarials to prevent the development of resistance to new malarial treatments and thus decrease treatment expenses. This way, financial, material and human resources can be allocated to other health issues that currently go unnoticed.