Chordoma: Understanding Your Pathology Report

Section Editor: Bibianna Purgina MD FRCPC
October 6, 2026

Chordoma is a rare, slow-growing bone cancer. It develops from cells left over from the notochord, a structure that guides spine formation before birth. The notochord normally disappears as the spine forms, but small groups of its cells can remain inside the bones of the spine and skull. Chordoma develops from these leftover cells.

Chordomas almost always develop along the body’s midline, in the bones of the spine and skull base. The two most common locations are the sacrum, the triangle-shaped bone at the bottom of the spine, and the clivus, a bone at the base of the skull. Most people diagnosed are between 40 and 70 years old, although chordoma can also occur in children.

Chordoma is a type of sarcoma. It grows slowly but tends to come back in the same place after surgery, and it can spread to other parts of the body, sometimes many years later.

This article explains how doctors diagnose chordoma and what the type, margins, and other findings in your pathology report mean.

What are the types of chordoma?

Your report will name one of three types. The type is one of the most important findings, because the three behave very differently:

Conventional chordoma. This is by far the most common type. It grows slowly, and many people live for years after diagnosis. Some conventional chordomas contain areas that look like cartilage, and these were once called chondroid chordoma. They are now considered part of the conventional type.
Poorly differentiated chordoma. This rare type usually affects children and young adults and most often develops in the skull base or upper spine. It grows faster and has a less favorable outlook.
Dedifferentiated chordoma. In this rare type, part of a conventional chordoma has changed into a fast-growing cancer that no longer looks like chordoma. It has the least favorable outlook.

What causes chordoma?

For most people, no cause is found. Chordoma is linked to a gene called TBXT, which makes a protein called brachyury. Brachyury is essential for forming the notochord before birth and is reactivated in chordoma cells.

Most chordomas occur in people with no family history. Rarely, chordoma runs in families, often linked to an extra copy of the TBXT gene. Children with tuberous sclerosis complex, an inherited condition, also have a higher risk. Your team may discuss genetic assessment if several family members have been affected.

What are the symptoms of chordoma?

Because chordoma grows slowly, symptoms often develop gradually, and the tumor may be large when found. The symptoms depend on where it is:

Sacrum. Low back or tailbone pain, and later problems with bladder or bowel control or numbness in the legs or buttocks.
Skull base. Headaches, double vision, difficulty swallowing, or other problems caused by pressure on the nerves at the base of the brain.
Spine. Back or neck pain, and sometimes weakness or numbness if the tumor presses on the spinal cord.

How is the diagnosis made?

MRI and CT show a tumor in the midline of the spine or skull base, often extending into the surrounding soft tissue. The diagnosis is confirmed with a biopsy, which should be done at the center that will perform the final surgery. Chordoma cells can grow along the biopsy needle track, so the biopsy track is planned to be removed with the tumor later.

Under the microscope, conventional chordoma is made of large cells arranged in cords and clusters within a soft, blue-gray background described as myxoid. Many cells contain small bubbles in their cytoplasm (the body of the cell). These are called physaliphorous cells, from a Greek word meaning bubble-bearing, and they are a characteristic feature of chordoma.

Poorly differentiated chordoma looks different. It is made of sheets of more abnormal cells, and the bubbly cells are usually absent. Dedifferentiated chordoma contains an area of conventional chordoma next to a high-grade cancer that looks like another type of sarcoma.

Immunohistochemistry

Immunohistochemistry is a test that uses antibodies to show which proteins tumor cells make. For chordoma, it is essential because it separates chordoma from other tumors in the same locations. Your report may include some of the following:

Brachyury. This protein is found in the nucleus of chordoma cells and is the most useful stain for this diagnosis. It is rarely found in other tumors, so a positive result strongly supports chordoma.
Cytokeratins and EMA. These proteins are usually positive in chordoma. They help separate it from chondrosarcoma, a cartilage cancer that can develop in the skull base and look similar.
INI1. This protein is normally present. Loss of INI1 staining defines poorly differentiated chordoma.

In dedifferentiated chordoma, the high-grade part often loses brachyury staining, while the conventional part keeps it.

Tumor extension

Large chordomas often break through the bone into the surrounding soft tissue, muscle, or nearby organs. This is called extraosseous extension, and your report may describe it.

The report may also note whether the tumor has grown from one bone segment into another. This is important for tumors of the sacrum and spine, which are made of several connected bones, because it raises the stage.

Margins

A margin is the edge of tissue cut by the surgeon. For chordoma, margins matter more than almost any other finding. Removal of the whole tumor in one piece with negative margins is the treatment most strongly linked to a lower chance of the tumor coming back.

Negative margin. No tumor cells are seen at the cut edge. The report may give the distance between the tumor and the closest margin.
Positive margin. Tumor cells reach the cut edge, and some tumor may remain. This raises the chance of the tumor coming back, and radiation therapy is usually recommended.

Chordomas of the skull base usually cannot be removed in one piece, because of the nearby brain, nerves, and blood vessels. They are often removed in many small pieces, and the pathologist cannot assess margins in that situation. How much tumor remains is then judged with MRI after surgery.

Lymph nodes

Chordoma rarely spreads to lymph nodes, so doctors usually do not remove them. When no nodes are examined, the report may say that the nodal stage was not assigned. When chordoma spreads, it more often travels through the bloodstream to the lungs, bones, or liver.

Stage

Bone cancers are staged using the TNM system from the American Joint Committee on Cancer (AJCC), 8th edition. Most chordomas develop in the sacrum and spine, which have their own staging rules. These rules depend on how many bone segments are involved and whether the tumor extends beyond the bone. For chordomas in the skull, the stage depends mainly on size, with 8 cm as the dividing line.

What is the prognosis?

The outlook for chordoma depends most on the type, the location, and whether the whole tumor can be removed.

Conventional chordoma. Because it grows slowly, many people live for years after diagnosis, and the median survival is around 6 to 7 years. About 2 in 3 people whose tumor is removed in one piece with negative margins are alive five years later, compared with about half of people overall.
Poorly differentiated chordoma. The outlook is less favorable, particularly in children, and these tumors are treated more intensively.
Dedifferentiated chordoma. This type has the least favorable outlook, with a median survival of a little over a year in published series.

The tumor comes back in the same place in a substantial number of people, especially when it could not be removed in one piece. Spread to other parts of the body can occur years after treatment, so follow-up continues for a long time. These figures describe groups of people and cannot predict what will happen to one person.

What happens after the diagnosis?

Chordoma is best treated at a center with experience in this rare cancer, by a team that includes spine or skull base surgeons and radiation oncologists.

Surgery. Removing the whole tumor in one piece with a rim of normal tissue, called en bloc resection, is the preferred treatment. For sacral tumors, this can affect the nerves that control the bladder, bowel, and legs, and your surgeon will discuss what to expect.
Radiation therapy. Chordoma needs high doses of radiation. Proton therapy or carbon ion therapy, which deliver high doses while sparing nearby tissue, are commonly used before or after surgery, or instead of surgery when it is not possible.
Chemotherapy. Standard chemotherapy works poorly for conventional chordoma and is not routinely used. It may be part of treatment for poorly differentiated or dedifferentiated chordoma.
Clinical trials. Researchers are studying targeted drugs and immunotherapy, particularly for tumors that come back or spread.
Follow-up. Regular MRI of the original site and chest imaging continue for many years.

Questions to ask your doctor

Which type of chordoma do I have: conventional, poorly differentiated, or dedifferentiated?
Was brachyury staining done to confirm the diagnosis?
Was the tumor removed in one piece, and were all the margins negative?
Will I need radiation therapy, and would proton therapy be an option?
How might surgery affect my bladder, bowel, or leg function?
Has the cancer spread anywhere else?
How often will I need follow-up imaging, and for how many years?