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The purpose of this study is to make the case for the utility of decision support systems (DSS) in the diagnosis of malaria and to conduct a case comparison of the effectiveness of the fuzzy and the AHP methodologies in the medical diagnosis of malaria, in order to provide a framework for determining the appropriate kernel in a fuzzy-AHP hybrid system. The combination of inadequate expertise and sometimes the vague symptomatology that characterizes malaria, exponentially increase the morbidity and mortality rates of malaria. The task of arriving at an accurate medical diagnosis may sometimes become very complex and unwieldy. The challenge therefore for physicians who have limited experience investigating, diagnosing, and managing such conditions is how to make sense of these confusing symptoms in order to facilitate accurate diagnosis in a timely manner. The study was designed on a working hypothesis that assumed a significant difference between these two systems in terms of effectiveness and accuracy in diagnosing malaria. Diagnostic data from 30 patients with confirmed diagnosis of malaria were evaluated independently using the AHP and the fuzzy methodologies. Results were later compared with the diagnostic conclusions of medical experts. The results of the study show that the fuzzy logic and the AHP system can successfully be employed in designing expert computer based diagnostic system to be used to assist non-expert physicians in the diagnosis of malaria. However, fuzzy logic proved to be slightly better than the AHP, but with non-significant statistical difference in performance.