The purpose of this study was to evaluate qualitatively and quantitatively the degeneration of Purkinje cells in the cerebellum of small ruminants affected with natural scrapie. The cerebellum of ewes and goats with clinical signs of scrapie were examined by immunochemistry for the accumulation of PrPsc, a specific marker for prion diseases and Calbindin-28k protein, a specific marker for Purkinje cells. Ewes (ARR/ARR) and goats without neurological diseases were used as negative controls. Results revealed that there was a significant loss of dendritic trees of Purkinje cells in the molecular layer and the cell body degeneration in the cellular layer in scrapie-infected animals. The decrease in the number of Purkinje cells in the cerebellum were estimated to 34.5 and 32.8% in sheep and goats, respectively. It is concluded that Purkinje cell degeneration is associated with motor disorders and ataxia in TSE infected animals.