We report a case of embryonal tumor with novel inclusion bodies occurring in the cerebellum of a 12-year-old girl. The tumor was histopathologically composed of small undifferentiated cells intermingled with a small number of rhabdoid cells, which had an ultrastructural feature of intermediate filament whorls. Immunohistochemically, the neoplasm showed a polyphenotype, including glial fibrillary acidic protein (GFAP), S-100, synaptophysin, chromogranin A, cytokeratin, vimentin, smooth muscle actin, and desmin. However, epithelial membrane antigen (EMA) immunoreactivity was absent. The MIB-1 labeling index was high (25.6%). Ultrastructurally, there was no evidence of neuronal or myogenic differentiation. The small neoplastic cells contained numerous small intracytoplasmic inclusions stained pink by eosin and red by Masson's trichrome stain. The inclusion body was a densely packed, granulovesicular structure at the electron microscopic level, and was immunoreactive for vimentin, GFAP, desmin, and actin. Reverse transcription-PCR and immunohistochemistry showed the expression of INI1 at the RNA and protein levels, respectively. In conclusion, this tumor was differentiated from atypical teratoid/rhabdoid tumor by the absence of EMA and the presence of INI1 mRNA and protein, and diagnosed as an unclassified, embryonal tumor. Eosinophilic, granulovesicular inclusions of the tumor cells are novel cytoplasmic inclusions in the brain tumor.