We recently produced transgenic mice that expressed an abnormally expanded polyglutamine (polyQ) specifically in cerebellar Purkinje cells (polyQ mice). The polyQ mice showed inclusion body formation, cerebellar atrophy and severe ataxia. Here we analyzed polyQ mice using immunohistochemistry, immunoelectronmicroscopy and electrophysiology. A diffuse form of polyQ was detected in the nucleus. Interestingly, ubiquitinated large inclusions were located close to, but apparently outside of the soma of Purkinje cells. Infusion of lucifer yellow into Purkinje cells clearly indicated the traffic between the periplasmic inclusions and soma of Purkinje cells. To examine whether the formation of periplasmic inclusions was an active process or a result of cell death, the polyQ mouse cerebellum was immunolabeled for cleaved caspase-3, a marker of apoptosis. Interestingly, no Purkinje cells in P80 polyQ mice immunoreacted with the antibody. The results were substantiated by electrophysiological assay, which showed that P80 Purkinje cells with large periplasmic inclusions were functionally active: excitatory postsynaptic currents (EPSCs) were reliably evoked upon electrical stimulation of parallel fibers (PFs) or climbing fibers (CFs), and current injection into Purkinje cells generated action potentials; however, the frequency of action potentials in response to various volumes of current injection was consistently lower in polyQ mice than in wild-type animals, and aberrant innervation by multiple CFs was detected in polyQ mouse Purkinje cells. These results suggest that Purkinje cells with periplasmic inclusions were not apoptotic, but their functions were substantially impaired, which could contribute to the severe ataxic phenotype.