How Are Gastrointestinal Stromal Tumors Diagnosed?

Gastrointestinal stromal tumors (GISTs) are often found because a person is having signs or symptoms. Others are found during exams or tests for other problems. If cancer is suspected, you will need further tests to confirm the diagnosis.

Medical history and physical exam

The doctor will ask you questions about your medical history, including your symptoms (eating problems, pain, bleeding, etc.), possible risk factors, family history, and other medical conditions.

Your doctor will give you a thorough physical exam to get more information about the possible signs of a GIST, like a mass in the abdomen, or other health problems.

If there is a reason to suspect that you may have a GIST (or other type of GI tumor), the doctor will use imaging tests or endoscopy exams to help find out if it is cancer or something else. If it is a GIST, further tests will be done to help determine the extent (stage) of the cancer.

Imaging tests

Imaging tests use x-rays, magnetic fields, or radioactive substances to create pictures of the inside of the body. Imaging tests may be done for a number of reasons, including:

  • To help find out if a suspicious area might be cancer
  • To learn how far cancer has spread
  • To help determine if treatment has been effective
  • To look for signs that the cancer has come back

Most patients who have or may have cancer will have one or more of these tests.

Barium x-rays

Barium x-rays are not used as much today as in the past. In many cases they are being replaced by endoscopy – where the doctor actually looks into your colon or stomach with a narrow fiber-optic scope (see below).

For these tests, a chalky solution containing barium is used to coat the inner lining of the esophagus, stomach, and intestines. This makes abnormalities of the lining easier to see on x-ray. These tests are sometimes used to diagnose GI tumors, but they can miss some small intestine tumors.

You will probably have to fast starting the night before the test. If the colon is being examined, you might need to take laxatives and/or enemas to clean out the bowel the night before or the morning of the exam.

Barium swallow: This test is often the first test done if someone is having a problem swallowing. For this test, you drink a liquid containing barium to coat the inner lining of the esophagus, A series of x-rays is then taken over the next few minutes.

Upper GI series: This test is similar to the barium swallow except that x-rays are taken after the barium has time to coat the stomach and the first part of the small intestine. To look for problems in the rest of the small intestine, more x-rays can be taken over the next few hours as the barium passes through the intestines. This is called a small bowel follow through.

Enteroclysis: This test is another way to look at the small intestine. A thin tube is passed through the mouth or nose, down your esophagus, and through your stomach into the start of the small intestine. Barium is sent through the tube, along with a substance that creates more air in the intestines, causing them to expand. Then x-rays are taken of the intestines. This test can give better images of the small intestine than a small bowel follow through, but it is also more uncomfortable.

Barium enema: This test (also known as a lower GI series) is used to look at the inner surface of the large intestine. For this test, the barium solution is given through a small, flexible tube inserted in the anus while the patient is lying on the x-ray table. When the colon is about half full of barium, the patient rolls over so the barium spreads throughout the colon. For a regular barium enema, x-rays are then taken. After the barium is put in the colon, air may be blown in to help push the barium toward the wall of the colon and better coat the inner surface. Then x-rays are taken. This is called an air-contrast barium enema or double-contrast barium enema.

Computed tomography (CT) scan

The CT scan is an x-ray test that produces detailed, cross-sectional images of your body. Instead of taking one picture, like a standard x-ray, a CT scanner takes many pictures as it rotates around you. A computer then combines these into images of slices of the part of your body that is being studied. Unlike a regular x-ray, a CT scan creates detailed images of the soft tissues in the body.

A CT scanner has been described as a large donut, with a narrow table in the middle opening. You will need to lie still on the table while the scan is being done. CT scans take longer than regular x-rays, and you might feel a bit confined by the ring while the pictures are being taken.

Before the test, you may be asked to drink 1 to 2 pints of an oral contrast liquid. This helps outline your digestive tract so that certain areas are not mistaken for tumors. You may also receive an intravenous (IV) line so that a different kind of contrast dye can be injected. This helps better outline blood vessels in your body.

Some people are allergic to the dye and get hives, a flushed feeling, or, rarely, more serious reactions like trouble breathing and low blood pressure. Medicines can be given to help prevent or treat allergic reactions, so be sure to let the doctor know before the scan about any allergies or previous reactions you have had to contrast material used for x-rays.

CT scans take longer than regular x-rays. The test is painless, but you may find it uncomfortable to hold still in certain positions for minutes at a time.

CT scans can be useful in patients with GISTs to find the location and size of a tumor, as well as to see if it has spread into the abdomen or the liver.

In some cases, CT scans can also be used to guide a biopsy needle precisely into a suspected cancer. However, this can be risky if the tumor might be a GIST (because of the risk of bleeding and a possible increased risk of tumor spread), so these types of biopsies are usually done only if the result might affect the decision on treatment. (See the biopsy information below.)

Magnetic resonance imaging (MRI) scan

MRI scans use radio waves and strong magnets instead of x-rays. The energy from the radio waves is absorbed and then released in a pattern formed by the type of tissue and by certain diseases. A computer translates the pattern into a very detailed image of parts of the body. A contrast material might be injected just as with CT scans, but is used less often.

MRI scans are a little more uncomfortable than CT scans. They take longer – often up to an hour. You have to lie inside a narrow tube, which is confining and can upset some people with a fear of enclosed spaces (claustrophobia). Newer, more open MRI machines can help with this, although the images may not be as sharp in some cases. The machine also makes buzzing and clicking noises that some people might find disturbing. Some places will provide earplugs to help block this noise out.

MRI scans can sometimes be useful in people with GISTs to help find the extent of the cancer in the abdomen, but usually CT scans are enough. MRIs can also be used to look for cancer that has come back (recurrence) or spread (metastasis) to distant organs, particularly in the brain or spine.

Positron emission tomography (PET) scan

For a PET scan, a radioactive substance (usually a type of sugar related to glucose, known as FDG) is injected into the blood. The amount of radioactivity used is very low. Because cancer cells in the body grow quickly, they absorb large amounts of the radioactive sugar. After about an hour, you will be moved onto a table in the PET scanner. You lie on the table for about 30 minutes while a special camera creates a picture of areas of radioactivity in your body.

PET scan images are not finely detailed like CT or MRI images, but a PET scan can look for possible areas of cancer spread in all areas of the body at once. Some newer machines are able to perform both a PET and CT scan at the same time (PET/CT scan). This lets the doctor see areas that “light up” on the PET scan in more detail.

PET scans can be useful for looking at GISTs, especially if the results of CT or MRI scans aren’t clear. This test also can be used to look for possible areas of cancer spread to help determine if surgery is an option.

PET scans can also be helpful in finding out if a drug treatment is working, as they can give an answer quicker than CT or MRI scans. The scan is usually obtained about 4 weeks after starting the medicine. If the drug is working, the tumor will stop taking up the radioactive sugar. If the tumor still takes up the sugar, your doctor may decide to change your drug treatment.


For these tests, the doctor puts a flexible lighted tube (endoscope) with a tiny video camera on the end into the body. The camera sends pictures to a video screen, so that the doctor can clearly see any masses (tumors) in the lining of the digestive tract. If abnormal areas are found, small pieces can be biopsied (removed) through the endoscope. The biopsy samples can be looked at under the microscope to find out if they contain cancer and if so, what kind of cancer it is.

GIST tumors are often below the inner lining (mucosa) of the GI tract. This makes them harder to see with endoscopy than more common GI tract tumors, which typically start in the mucosa. The doctor may see only a bulge under the normally smooth surface if a GIST is present. GISTs that are below the mucosa are also harder to biopsy through the endoscope. This is one reason only about half of GISTs are diagnosed before surgery.

If the tumor breaks through the inner lining of the GI tract and is easy to see on endoscopy, there is a greater chance that the GIST is cancerous (malignant).

Upper endoscopy

For this procedure, patients are usually given medicines through an intravenous (IV) line to sedate them (make them sleepy). Then an endoscope is passed through the mouth to look at the inner lining of the esophagus, stomach, and first part of the small intestine. Biopsy samples may be taken from any abnormal areas.

Upper endoscopy can be done in a hospital, in an outpatient surgery center, or in a doctor’s office. It usually takes 10 to 20 minutes, but it might take longer if a tumor is seen or if biopsy samples are taken. If medicine is given to make you sleepy for the procedure, you will need someone you know to drive you home (not just a cab).

This test is also known as EGD (short for esophagogastroduodenoscopy).

Colonoscopy (lower endoscopy)

For this test, a type of endoscope known as a colonoscope is inserted through the anus and up into the colon. This lets the doctor look at the lining of the entire rectum and colon and to take biopsy samples from any abnormal areas.

To get a good look at the inside of the colon, it must be empty and cleaned out before the test. This often means drinking a large amount of a liquid laxative the evening before and spending much of the night in the bathroom. Sometimes more liquid needs to be drunk or enemas are used the morning of the procedure to make sure the bowels are empty.

You will be given intravenous (IV) medicine to make you feel relaxed and sleepy during the procedure. A colonoscopy can be done in a hospital, in an outpatient surgery center, or in a doctor’s office. It usually takes 15 to 30 minutes, but it can take longer if a tumor is seen and/or a biopsy taken. Because medicine is given to make you sleepy for the procedure, you will need someone you know to drive you home (not just a cab).

Capsule endoscopy

Unfortunately, neither upper nor lower endoscopy can reach all areas of the small intestine. Capsule endoscopy is one way to look at the small intestine.

This procedure does not actually use an endoscope. Instead, the patient swallows a capsule (about the size of a large vitamin pill) that contains a light source and a very small camera. Like any other pill, the capsule goes through the stomach and into the small intestine. As it travels through the intestine (usually over about 8 hours), it takes thousands of pictures. These images are transmitted electronically to a device worn around the person’s waist. The pictures can then be downloaded onto a computer, where the doctor can view them as a video. The capsule passes out of the body during a normal bowel movement and is discarded.

This test requires no sedation – the patient can just continue normal daily activities as the capsule travels through the GI tract. This technique is fairly new, and the best ways to use it are still being studied. One disadvantage is that any abnormal areas seen can’t be biopsied during the test.

Double balloon enteroscopy (endoscopy)

This is another way to look at the small intestine. The small intestine is too long and has too many curves to be examined well with regular endoscopy. This method gets around these problems by using a special endoscope that is made of 2 tubes, one inside the other.

The patient is given intravenous (IV) medicine to relax them, or even general anesthesia (so that they are asleep). The endoscope is then inserted either through the mouth or the anus, depending on if there is a specific part of the small intestine to be examined.

Once in the small intestine, the inner tube, which has the camera on the end, is advanced forward about a foot as the doctor looks at the lining of the intestine. Then a balloon on the end of the endoscope is inflated to anchor it. The outer tube is then pushed forward to near the end of the inner tube and is anchored in place with a second balloon. The first balloon is deflated and the endoscope is advanced again. This process is repeated over and over, letting the doctor see the intestine a foot at a time. The test can take hours to complete.

This test may be done along with capsule endoscopy. The main advantage of this test over capsule endoscopy is that the doctor can take a biopsy if something abnormal is seen. Like other forms of endoscopy, because you are given medicine to make you sleepy for the procedure, someone you know will need to drive you home (not just a cab).

Endoscopic ultrasound

This is a type of imaging test that uses an endoscope. Ultrasound uses sound waves to take pictures of parts of the body. For most ultrasound exams, a wand-like probe (called a transducer) is placed on the skin. The probe gives off sound waves and detects the pattern of echoes that come back.

For an endoscopic ultrasound, the ultrasound probe is on the tip of an endoscope. This allows the probe to be placed very close to (or on top of) a tumor in the wall of the digestive tract. Like a regular ultrasound, the probe gives off sound waves and then detects the echoes that bounce back. A computer then translates the pattern of echoes into an image of the area being looked at.

Endoscopic ultrasound can be used to find the precise location of the GIST and to determine its size. It is useful in finding out how deeply a tumor has grown into the wall of the digestive tract. The test can also help show if the tumor has spread to nearby lymph nodes or has started growing into other tissues nearby. In some cases it may be used to help guide a biopsy (see below).

This procedure is usually done under sedation (medicine is given to make the patient sleepy). Because of this, the patient needs to have someone they know drive them home (not just a cab).


Even if a mass is found on an imaging test such as a barium x-ray or CT scan, these tests cannot tell if the mass is a GIST, some other type of tumor (benign or cancerous), or some other condition (like an infection). The only way to know what it is for sure is to remove cells from the abnormal area. This procedure is called a biopsy. The cells are then sent to a lab, where a doctor called a pathologist looks at them under a microscope and does other tests on them.

GISTs are often fragile tumors that tend to break apart and bleed easily. If the doctor suspects a tumor may be a GIST, biopsies must be done carefully and are usually done only if they will help determine treatment options, because of concerns the biopsy might cause bleeding or possibly increase the risk of cancer spreading.

There are several ways to biopsy a GI tract tumor.

Endoscopic biopsy

Biopsy samples can be obtained through an endoscope. When a tumor is found, the doctor can insert biopsy forceps (pincers or tongs) through the tube to take a small sample of the tumor.

Even though the sample will be very small, doctors can often make an accurate diagnosis. However, with GISTs, sometimes the biopsy forceps can’t go deep enough to reach the cancer because the tumor is underneath the lining of the intestine or stomach.

Bleeding from a GIST after a biopsy is rare, but it can be a serious problem. If this occurs, doctors can sometimes inject drugs into the tumor through the endoscope to constrict blood vessels and stop the bleeding.

Fine needle aspiration (FNA) biopsy

In some patients, a biopsy is done with a thin, hollow needle. The most common way to do this is during an endoscopic ultrasound. The doctor uses the ultrasound image to guide a needle on the tip of the endoscope into the tumor. Less commonly, the doctor may place a needle through the skin and into the tumor while guided by an imaging test such as a CT scan.

Surgical biopsy

If a sample can’t be obtained from an endoscopic or FNA biopsy or if the result of a biopsy wouldn’t affect treatment options, your doctor might recommend waiting until surgery to remove the tumor to get a sample of it.

If the surgery is done through a large cut (incision) in the abdomen, it is called a laparotomy. In some cases, the tumor may be sampled (or small tumors can be removed) using a thin lighted tube that allows the surgeon to see inside the belly through a small incision called a laparoscope. The surgeon can use long, thin surgical instruments that are passed through other small incisions in the abdomen. This is known as laparoscopic or keyhole surgery.

Testing the biopsy sample

Once a tumor sample is obtained, a pathologist looks at it under a microscope. The pathologist may suspect that a tumor is a GIST, but often can’t be sure without further tests.

For a special test called immunohistochemistry, a part of the sample is treated with man-made antibodies that will attach only to the KIT protein (also called CD117). The antibodies cause color changes if the KIT protein is present, which can be seen under a microscope. Most GIST cells have this protein, but cells of most other types of cancer do not, so this test can help determine whether a GI tumor is a GIST or not. If the tumor cells do not contain KIT, they will be checked to see if they have too much of the PDGFRA protein. This is found in about 5% to 10% of GISTs.

If the doctor is still unsure if the tumor is a GIST, other tests might be done on the biopsy sample to look for mutations in the c-kit or PDGFRA genes themselves.

If a GIST is diagnosed, the doctor will also look at the cancer cells in the sample to see how many of them are actively dividing into new cells. This is known as the mitotic rate. A low mitotic rate means the cancer cells are growing and dividing slowly, while a high rate means they are growing quickly. The mitotic rate is an important part of the stage of the cancer (see “ How are gastrointestinal stromal tumors staged?”).

Blood tests

Your doctor may order some blood tests if he or she thinks you may have a GIST. There are no blood tests that can tell if a person has a GIST. These tumors do not release any known substances in the blood that can be used to diagnose a GIST or to measure its response to treatment.

However, blood tests can sometimes point to a possible tumor (or to its spread). For example, a complete blood count (or CBC) can tell if you have a low red blood cell count (are anemic). Some people with GIST may become anemic because of bleeding from the tumor. Abnormal liver function tests may mean that the GIST has spread to your liver.

Blood tests are also done to check your overall health before you have surgery or while you get other treatments such as targeted therapy.

The American Cancer Society medical and editorial content team
Our team is made up of doctors and master’s-prepared nurses with deep knowledge of cancer care as well as journalists, editors, and translators with extensive experience in medical writing.

Last Medical Review: April 4, 2014 Last Revised: February 8, 2016

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