Malignant rhabdoid tumor (MRT) is a highly aggressive neoplasm that mostly occurs in childhood, characterized histologically by rhabdoid cells as shown by eosinophilic intracytoplasmic inclusions. Although it is known that rhabdoid cells co-express cytokeratin (CK) and vimentin, the distribution patterns of these two kinds of intermediate filaments and structural relationship between them are still not known. We investigated the subcellular distribution of CKs 8 and 18 and vimentin in MRT cell lines (Tm87-16, STM91-01, TTC549, and TC289) using confocal laser scanning microscopy and double immunofluorescence, in addition to ultrastructural examination. Vimentin was diffusely expressed in the cytoplasm of MRT cells, focally forming a filamentous network. In contrast, CKs 8 and 18 were partially expressed in the cytoplasm of MRT cells, forming globules or a few vague agglomerates. Three-dimensional images in TC289 cells revealed distinct distribution patterns of cytokeratin and vimentin, showing agglomerates of cytokeratins within the vimentin filament network. We conclude that these globules and agglomerates of CKs 8 and 18 correspond with the characteristic ultrastructural finding, showing cytoplasmic bundles of intermediate filaments concentrated in whorled arrays.