Objective To investigate the effect of ethanol exposure on the autophagy in cerebellar Purkinje cells. Methods With intubating pregnant mice ethanol daily from E5 until the pup’s birth, the animal models of prenatal alcohol exposure (PAE) were made. Totally 180 pups included control treatment and ethyl alcohol(EtOH) treatment were used in the study. On the other hand, the autophagy in cerebellar Purkinje cells in P7, P14 and P30 was investigated with transmission electron microscopy, immunofluorescent labeling and Western blotting technique. Results With electron microscopy, a numerous lysosome and autophagosomes were found in the Purkinje cells of alcohol exposure mice, with organelle injuries as well. Under light microscope, Purkinje cells changed lots after ethanol exposure, such as irregular arrangement, reduced dendritic branches and dentritic spines. The positive autophagy cells (PAC) and positive autophagy index (PAI) in ethanol treatment groups were obviously higher than that in control at either P7 or P14 (EM>P/EM><0.001) with dose dependency (EM>P/EM><0.001). In the meantime, PAC and PAI increased gradually with age increasing EM>(F/EM>=58.29,EM> P/EM><0.001). The coexpression of Beclin-1 and MAPLC3 in the same Purkinje cell suggested the Beclin-1’s regulation to the autophagy. Western blotting analysis supported the above results from immunocytochemistrys. Conclusion Autophagy is involved in the normal development and alcohol’s toxicological effects of cerebellar Purkinje cells. The prenatal ethanol exposure can induce the autophagy of Purkinje c