The goal of this article was to characterize the clinical evolution of scrapie in naturally affected sheep. Eighteen sheep with scrapie diagnosed by examination of 3rd eyelid biopsy and 12 control ewes were studied throughout the duration of their disease. Diagnosis was confirmed postmortem by histopathologic, immunohistochemical, and Western blot analysis of nervous tissue. Complete clinical examinations were performed every 2 weeks for each animal, of which 3 clinical examinations per animal are reported. Those clinical signs that showed a significant frequency within the corresponding clinical examination were considered representative of each stage of the disease (ie, early, middle, and late). The representative clinical signs for the early stage were hypoesthesia in the limbs, alteration of mental status, and a body condition score ,3. Remarkably, hypoesthesia in the limbs was one of the 1st signs appearing during the early clinical stage in the affected animals, even before the appearance of other signs. For the middle stage, representative signs were the same as those for the early stage, together with hyporreflexia in the limbs, cardiac arrhythmia, pruritus/wool loss, and the appearance of the nibbling reflex. Representative clinical signs for the late stage were the same as those for the early and middle stage, together with head tremors, hyperexcitability to external stimuli, ataxia or gait abnormalities, and teeth grinding. On the basis of these results, we propose the calculation of an objective clinical index that allows the differentiation among clinical stages and that could be useful for further studies. The usefulness of 3rd eyelid lymphoid tissue biopsies for sequential clinical studies in naturally scrapie-affected sheep is demonstrated.