Two cases of skull base chordoma (case 1, a 57-year-old woman; case 2, a 69-year-old woman) were investigated immunohistochemically and ultrastructurally. The tumors showed histopathological features typical of chondroid chordoma and contained both classical chordomatous and hyaline cartilaginous components. Tumor cells were immunoreactive for cytokeratin, vimentin, and S-100 protein, but negative for microtubule-associated protein 2 and class III beta-tubulin (tub-B3). Tumor cells of case 2 were immunoreactive for tau-protein and class II beta-tubulin (tub-B2), whereas those of case 1 were negative. Ultrastructurally, tumor cells in both cases showed the presence of abundant glycogen granules, well-developed intracellular organelles, and desmosome-like junctions. In case 2, several microtubules were closely packed and ran parallel or in random directions within the dilated cisterns of rough-surfaced endoplasmic reticulum (rough ER). "Microtubules within rough ER" has been described in several neoplasms, including classical and chondroid chordomas. Although previous reports documented the tub-B3 immunoreactivity in chordomas, our results suggested that, in our case 2, the predominant isoform of beta-tubulin in microtubules within rough ER was not tub-B3 but tub-B2.