This is a unique case of chondroid chordoma arising in the sacrococcygeal area of an asymptomatic man. S100 protein was detected in both chondroid and chordoid tissues; epithelial membrane antigen (EMA) and cytokeratin were present in abundant amounts in the cytoplasm of chordoma cells but not in chondroid cells. The presence of cytokeratin and EMA in chordoma implies the epithelial nature of the tumor and is extremely helpful as a differential marker for chordoma. I suggest that EMA, cytokeratin, and S100 protein should be used conjunctively to provide a resolution for difficult diagnostic problems when dealing with chordomas, especially with their variants, such as chondroid chordomas, which often cause further confusion.