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This paper describes a fuzzy approach to computer aided medical diagnosis in a clinical context. It introduces a formal view of diagnosis in clinical settings and shows the relevance and possible uses of fuzzy cognitive maps and fuzzy logic. A constraint satisfaction method is introduced which uses the temporal uncertainty in symptom durations that may occur with particular diseases. Together with fuzzy symptom descriptions, the method results in an estimate of the stage of a disease if the temporal constraints of the disease in relation to the occurrence of the symptoms are satisfied. The approach is evaluated through simulation experiments showing the effects of symptom ordering, temporal uncertainty and symptom strengths on the diagnosis efficiency. The method is effective and can be developed further using second order (Type 2) fuzzy logic to better represent uncertainty in the clinical context thus improving differential diagnosis accuracy.