Background: Purkinje cells (PCs) pathology is important in cerebellar disorders like ataxia. The spatial arrangement of PCs after different treatments has not been studied extensively. Immunohistochemistry (IHC) analysis of cerebellum can give a proper tool for explaining the pathophysiology of PCs in ataxia. Here we stereologically analysed the 3-dimensional spatial arrangement of PCs in the cerebellum of rats after ataxia induction with 3-acetylpyridine (3-AP). Materials and methods: Ataxia was induced in rats by intraperitoneal injection of 3-AP (65 mg/kg). Spatial arrangement of PCs for differences in ataxic rats with (3-AP-SC) or without (3-AP) Sertoli cells (SCs) transplantation was evaluated using second-order stereology. The IHC method by using antibodies to anti-calbindin in the cerebellum was applied. Results: Our results showed that a random arrangement is at larger distances between PCs in 3-AP and 3-Ap-SC groups. Therefore the PCs are not normally arranged after 3-AP and SCs transplantation stored the spatial arrangements of the cells after ataxia induction in rats. IHC analyse shows that number of PCs was significantly improved after the SC transplantation. Conclusions: Segregation of PCs can be observed at some areas in the ataxic rats’ cerebellum. However, the spatial arrangement of PCs was unchanged in SCs transplanted rats. (Folia Morphol 2018; 77, 2: 194–200)