Rare diseases are a real public health problem for hospitals and also for primary care. We describe some metaphor-based diagnosis procedures, such as: “When you hear hoof beats don’t always think horses, sometimes they could be zebras”, or that one about the antiquarian who recognised a museum masterpiece while walking in the Rastro (Madrid). The “lightning diagnoses” by Skoda are an important historic record. T. Greenhalgh has tried to cover the gap between evidence based medicine and the intuitive diagnosis. We point out some clinical epidemiology rules in order to improve their early detection by family practitioners and paediatricians. In our opinion, the training in the diagnosis of rare diseases has to be different for primary care level and for hospital doctors. Concept maps are useful for diagnosis in primary care clinics.

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