Chordoma is best seen on MRI but can also be visualized with a CT scan. Chordoma cannot be seen on x-ray.

Although chordoma does have a distinctive appearance on MRI, Benign Notochordal Cell Tumors (BNCT) and Chondrosarcoma may appear similar. The only way to confirm the diagnosis is to perform a biopsy. This can be safely done in suspected sacral and mobile spine chordoma by CT guided needle biopsy. In clival (skull base) chordoma, biopsy can be difficult, and the surgeon may decide to remove the tumor.

Open biopsy, where the surgeon opens the skin and removes a piece of the tumor for testing should never be done. During an open biopsy tumor cells will likely spill, contaminating the wound, allowing the chordoma to seed, and decreasing the chance for a good outcome.