Extraskeletal chordoma arising within soft tissue is a rare occurrence. We report a case of chordoma that is unusual both for its location within the subcutaneous soft tissue of the sacrococcygeal region without involvement of adjacent bones and for the presence of eosinophilic roundish inclusion bodies within the cytoplasm of tumor cells. These bodies revealed immunoreactivity for cytokeratin and a fibrillar, partly whorled structure on the electron microscopic examination, consistent with an intermediate filament-based composition. To our knowledge, this is the first report of chordoma featuring this cellular change although we do not know the significance of these bodies.