Tests for Brain and Spinal Cord Tumors in Children

Brain tumors are usually found because of signs or symptoms a child or teen is having. If the doctor suspects a tumor, exams and tests will be done to confirm the diagnosis.

Medical history and physical exam

If your child has symptoms that suggest a brain or spinal cord tumor, the doctor will:

  • Ask about your child’s medical history, focusing on the symptoms and how long your child has had them.
  • Do a neurologic exam to check the function of the brain and spinal cord, if possible.

Depending on the child’s age, the exam may test reflexes, sensation, muscle strength, vision, eye and mouth movement, coordination, balance, alertness, and other functions.

If the doctor thinks your child might have a brain tumor, imaging tests and a biopsy will often be needed to be sure. A primary care doctor or pediatrician may start with initial tests like an MRI or CT scan, or they may refer you to a specialist, such as a pediatric neuro-oncologist (a doctor who cares for children with brain tumors), neurosurgeon (a surgeon specializing in problems with the brain and spinal cord), or neurologist (a doctor who specializes in brain and nerve function), for these tests and any further work-up that is needed to make a diagnosis.

Imaging tests

Your doctors may order one or more imaging tests. These tests use x-rays, strong magnets, or radioactive substances to create pictures of internal organs such as the brain and spinal cord. The pictures may be looked at by doctors specializing in this field (neurosurgeons, neurologists, and neuroradiologists) as well as by your  primary care doctor or oncologist.

Magnetic resonance imaging (MRI) and computed tomography (CT) scans are used most often for brain diseases. These scans will almost always show a brain or spinal cord tumor, if one is present. Doctors can often also get an idea about what type of tumor it might be, based on how it looks on the scan and where it is in the brain or spinal cord.

MRI scans are the best way to look for tumors in the brain and spinal cord. MRI images are usually more detailed than those from CT scans (described below). But they do not show the bones of the skull as well as CT scans and therefore might not show the effects of tumors on the skull.

MRIs use radio waves and strong magnets instead of x-rays, so there is no radiation. A contrast material called gadolinium may be injected into a vein before the scan to help see details better.

MRI scans can take a long time, and they require a person to stay still for several minutes at a time. Some children might need medicine to help them relax or even go to sleep during the test.

Special types of MRI can be useful in some situations:

Magnetic resonance spectroscopy (MRS) measures biochemical changes in an area of the brain and displays them in graph-like results called spectra. It’s done as part of an MRI, so regular MRI pictures are taken at the same time.

MRS can help determine:

  • The type of tumor or how quickly it is likely to grow, by comparing the results for a tumor to normal brain tissue
  • Whether an area that still looks abnormal after treatment is more likely to be remaining tumor or scar tissue.

Magnetic resonance perfusion (MR perfusion) shows the amount of blood going through different parts of the brain, using a contrast dye injected quickly into a vein. Tumors often have a bigger blood supply than normal areas of the brain, and a faster growing tumor often needs more blood.

MR perfusion can help determine:

  • The best place to take a biopsy
  • Whether an area that still looks abnormal is more likely to be remaining tumor or scar tissue

Functional MRI (fMRI) looks for tiny blood flow changes in an active part of the brain. It’s like a standard MRI, except that your child will be asked to do certain tasks (such as answering simple questions or moving fingers) while the scans are being done.

fMRI can help determine:

  • Which part of the brain handles a function such as speech, thought, sensation, or movement so doctors can avoid these areas when planning surgery or radiation therapy.

Diffusion tensor imaging (DTI), also known as tractography, shows where the major pathways (tracts) of white matter (nerve fibers) are in the brain so surgeons can avoid these important parts of the brain when removing tumors.

Magnetic resonance angiography (MRA) and magnetic resonance venography (MRV): These special types of MRI may be done to look at the blood vessels (arteries and veins) in the brain. This can be useful before surgery to help plan an operation.

Susceptibility-weighted imaging (SWI) can be used to detect bleeding in the brain, either within a tumor or because of an injury or bleeding disorder. In the past, this was done using a test called gradient echo imaging, but now SWI is used most often.

Diffusion-weighted imaging (DWI) can be used to assess how aggressive a tumor is. It measures how quickly or slowly water moves through parts of the brain. If water moves slowly in a tumor this can mean there are more tumor cells, and the tumor may be more likely to be malignant.

A CT scan uses x-rays to make detailed cross-sectional images of the brain and spinal cord (or other parts of the body).

CT scans are not quite as good as MRI scans for looking at brain or spinal cord tumors, so they aren’t used as often. Still, there are instances where CT scans may have advantages over MRI scans:

  • CT scans take much less time than MRIs, which can be particularly helpful for children who have trouble staying still or if imaging is needed right away.
  • CT scans show greater detail of the bone structures near the tumor.
  • CT angiography (CTA), described below, can provide better details of the blood vessels in and around a tumor than MRA in some cases.

Before the scan, your child may get an injection of a contrast dye through an IV (intravenous) line. This helps better outline any tumors that are present.

CT angiography (CTA): For this test, your child may get an injection of contrast material through an IV line while they are in the CT scanner. The scan creates detailed images of blood vessels in the brain, which can help doctors plan surgery.

For a PET scan, your child will get an injection with a slightly radioactive sugar that collects mainly in tumor cells. A special camera is then used to create a picture of areas of radioactivity in the body. This radioactive substance leaves the body in a day or so. The picture made on a PET scan is not as detailed as a CT or MRI scan, but it can help tell whether abnormal areas seen on other tests are likely to be tumors. This test is more likely to be helpful for fast-growing (high-grade) tumors than for slower-growing tumors.

A PET scan can also be useful after treatment to help determine whether an area that still looks abnormal on an MRI is more likely to be remaining tumor or scar tissue. The remaining tumor might show up on the PET scan, while scar tissue will not.

Many centers now have machines that can do both a PET scan and a more detailed scan at the same time (PET/MRI or PET/CT).

PET scans are not used routinely for children with brain tumors but can help doctors check whether treatment is working or check for treatment-related changes such as radiation necrosis.

Brain tumor biopsy

Imaging tests such as MRI and CT scans may show an abnormal area that is likely to be a brain tumor or spinal cord tumor. Often, these scans can give the doctor a good idea of what type of tumor it is. But this can only be confirmed by removing some of the tumor tissue in a procedure called a biopsy and then doing lab tests on it.

A biopsy may be done as a procedure on its own, or it may be part of surgery to remove the tumor.

Sometimes the way a brain tumor looks on an imaging test makes it almost certain what type of tumor it is. If this is the case, your doctors will likely advise going right to surgery, if it can be done (see below). The neurosurgeon will remove as much of the tumor as possible, and part of it can then be tested in the lab to confirm the diagnosis and learn more about it.

If a tumor is in a part of the brain, such as the brain stem, that would make it hard to biopsy, an imaging test may give enough information about the tumor so that a biopsy is not needed.

The 2 main types of biopsies for brain tumors are:

A stereotactic (needle) biopsy may be used if, based on imaging tests, a biopsy sample is needed and removing the whole tumor might be too risky (such as with some tumors in vital areas, those deep within the brain, or other tumors that cannot be removed safely with surgery).

The biopsy is done under general anesthesia (while asleep).

The biopsy itself can be done in 2 main ways:

  • The most common approach is to get an MRI or CT scan and then use either markers (each about the size of a nickel) placed on different parts of the scalp, or facial and scalp contours, to create a map of the inside of the head. The neurosurgeon then makes an incision (cut) in the scalp and drills a small hole in the skull. Using an image-guidance system, they insert a hollow needle into the tumor to remove small samples of tissue.
  • In an approach that is used less often, a rigid frame is attached to the head. An MRI or CT scan is often used along with the frame to help the neurosurgeon guide a hollow needle into the tumor. This also requires an incision in the scalp and a small hole in the skull.

The biopsy samples are sent to a pathologist (a doctor specializing in diagnosing diseases with lab tests). The pathologist looks at them under a microscope (and might do other lab tests) to determine whether the tumor is benign or malignant (cancerous) and exactly what type of tumor it is. This helps determine the best course of treatment and the prognosis (outlook).

A preliminary diagnosis may be available the same day as the biopsy, although it often takes a few days to get more test results and a final diagnosis.

If imaging tests show the tumor can likely be treated with surgery, the neurosurgeon may do a craniotomy to remove all or most of the tumor instead of a needle biopsy. If removing all of the tumor would likely damage nearby important structures, removing most of the tumor, known as debulking, might be done instead.

For a preliminary diagnosis, small samples of the tumor are looked at right away by the pathologist while the patient is still in the operating room. This can help guide treatment, including whether further surgery should be done at that time. A final diagnosis is made within a few days in most cases.

Testing for gene mutations and other changes

Testing tumor cells (from biopsy or surgery samples) for changes in certain genes, chromosomes, or proteins has become increasingly important in diagnosing and treating brain tumors. It can help determine what type (or subtype) of tumor a person has, and sometimes it can help show whether certain treatments are more or less likely to be helpful. For example:

  • In gliomas, the grade of the tumor and gene changes in tumor cells can help doctors tell the difference between tumors like a pilocytic astrocytoma, which may have gene changes in BRAF, and a more difficult to treat or faster growing tumor called a diffuse midline glioma, which may have a mutation in H3K27M. Gene changes in IDH1, IDH2, NF1, NTRK1, NTRK2, NTRK3, ALK, ROS1, and MN1 also help distinguish different types of gliomas from one another.
  • In medulloblastoma, knowing whether there are gene changes in WNT, SHH, and TP53 can help doctors predict how a tumor grows and responds to treatment.
  • In atypical teratoid/rhabdoid tumors (AT/RT), gene changes in SMARCB1 and SMARCA4 can help doctors make the diagnosis and pick the best treatments.
  • In ependymomas, doctors often check for ZFTA-fusion status (formerly called RELA-fusion status) which can impact the treatment plan and outlook for these types of tumors.

You can read more about the kinds of tests that are done on biopsy or tissue samples in Testing Biopsy and Cytology Specimens for Cancer.

Lumbar puncture (spinal tap)

This test is used mainly to look for cancer cells in the cerebrospinal fluid (CSF), the liquid that surrounds the brain and spinal cord. It is recommended if a tumor has already been diagnosed as a type that can commonly spread through CSF, such as a medulloblastoma. Information from the spinal tap can help determine the best treatment options.

For this test, the doctor first numbs an area in the lower part of the back over the spine. The doctor may also recommend that the child be given medicine to make them sleep so the lumbar puncture can be done more easily and safely. A small, hollow needle is then placed between the bones of the spine to withdraw some of the fluid.

The fluid is sent to the lab to look for cancer cells. Other tests may be done on the fluid as well, depending on the type of tumor.

Lumbar punctures are usually very safe, but doctors have to make sure the test does not result in a large drop in fluid pressure inside the skull, which could possibly cause serious problems. For this reason, imaging tests such as CT or MRI scans are usually done first.

Blood and urine tests

Lab tests are rarely used to diagnose brain and spinal cord tumors. However, blood AFP and β-HCG levels can be used to diagnose a certain type of brain tumor called a germ cell tumor.

In most cases, especially if you or your child has been sick for some time, lab tests are used to check how well the liver, kidneys, and other organs are working. This is especially important before any treatment.

If chemotherapy or radiation is part of treatment, blood tests will be done routinely to check blood counts and for other side effects. In some cases, a dose may need to be adjusted or treatment may need to be stopped for a while to allow the body to recover.

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Developed by the American Cancer Society medical and editorial content team with medical review and contribution by the American Society of Clinical Oncology (ASCO).

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Huang A, Lindsay H, Tamrazi B, Adesina AM, Paulino AC, Pollack IF, et al. Chapter 22B: Tumors of the Central Nervous System: Embryonal and Pineal Region Tumors. In: Blaney SM, Adamson PC, Helman LJ, eds. Pizzo and Poplack’s Pediatric Oncology. 8th ed. Philadelphia, Pa: Lippincott Williams & Wilkins; 2021.

National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology: Pediatric Central Nervous System Cancers. v.3.2025 – September 2, 2025. Accessed at https://www.nccn.org/professionals/physician_gls/pdf/ped_cns.pdf on September 17, 2025.

Parsons DW, Pollack IF, Hass-Hogan DA, Paulino AC, Kralik SF, Desai, NK, et al. Chapter 22A: Gliomas, Ependymomas, and Other Nonembryonal Tumors of the Central Nervous System. In: Blaney SM, Adamson PC, Helman LJ, eds. Pizzo and Poplack’s Pediatric Oncology. 8th ed. Philadelphia, Pa: Lippincott Williams & Wilkins; 2021.

Last Revised: February 9, 2026

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