The first histologically confirmed case of a classic chordoma arising in a precursor benign notochordal lesion is presented and the differential diagnosis between benign and malignant notochordal lesions is discussed. A 57-year-old man presented with a classic chordoma in the coccyx. The resected specimen demonstrated a small intraosseous benign notochordal lesion in the coccyx, which was adjacent to the classic chordoma. Also seen were two separate, similar benign lesions in the sacrum. The classic chordoma consisted of multiple lobules that were separated by thin fibrous septa and that showed cords or strands of atypical physaliphorous cells set within an abundant myxoid matrix. In contrast, the benign lesions consisted of intraosseous sheets of bland physaliphorous cells without any extracellular matrix. The affected bone trabeculae showed sclerotic reactions. It was concluded that benign and malignant notochordal lesions can be distinguished microscopically.