A hole in the brain is almost never an empty gap. It is usually a pocket of fluid sitting where brain tissue used to be, so the real question is what damaged that tissue. The most common answers are a stroke, a bleed, a head injury, or an infection.1The Health Researcher’s Journal. A CASE REPORT OF 41-YEAR-OLD MALE WITH POST TRAUMATIC ENCEPHALOMALACIA Not every hole on a scan is damage, though. Some are normal fluid channels that have simply widened and stay the same for years.2American Journal of Neuroradiology. Subcortical Cystic Lesions within the Anterior Superior Temporal Gyrus: A Newly Recognized Characteristic Location for Dilated Perivascular Spaces And the word can mean very different things, from a scar left by an old injury to the microscopic sponge-like gaps of rare prion diseases.3PubMed Central. Cellular and Molecular Mechanisms of Prion Disease
What Fills the Space Where Brain Tissue Was Lost
When brain tissue is badly damaged, it softens and is cleared away. Doctors call this lost, softened tissue “encephalomalacia,” a word you may see on a scan report.4The Health Researcher’s Journal. A CASE REPORT OF 41-YEAR-OLD MALE WITH POST TRAUMATIC ENCEPHALOMALACIA Within a day of a stroke, the brain’s resident cleanup cells move into the damaged area and start removing debris.5PubMed Central. Phagocytosis of Microglia in the Central Nervous System Diseases Cleanup cells from the blood arrive around day 4 and peak in the following days, so clearing continues for about 2 weeks.6PubMed Central. Phagocytosis of Microglia in the Central Nervous System Diseases By the end, a pocket that once held brain tissue holds fluid instead.
That fluid is the same clear fluid that bathes the brain normally, and it shows up on MRI in the same shade as that normal fluid. The space doesn’t refill with new tissue because adult brain cells mostly cannot regrow to fill a large gap. The surrounding brain can still learn to take over some jobs, which is why recovery often continues after the damage is done.
The hole also leaves marks on the brain around it. The edge usually forms scar tissue, which reports call “gliosis.”7PubMed Central. Clinical characteristics of cystic encephalomalacia in children On some image types, that scar rim appears as a brighter outline. Nearby brain can shrink, so the fluid spaces next to the hole look larger and the surface layer looks thinner.8Journal of Neurosciences in Rural Practice. Multicystic encephalomalacia secondary to head trauma
Strokes and Bleeds Are the Most Common Cause
Brain tissue that loses its blood supply dies within hours, and that is what a stroke is. Bleeding into brain tissue damages it too, and blood can seep into the dying area.9PubMed Central. Encephalomalacia from Physical Trauma in an Adult: A Case Report and Review of Literature After either kind of stroke, cleanup follows the timeline described above and leaves a cavity.10PubMed Central. Phagocytosis of Microglia in the Central Nervous System Diseases
Tiny strokes deep in the brain can leave small holes that some people never noticed when they happened. A report may describe them as “old” or “chronic” infarcts. Finding one usually prompts checks of blood pressure, cholesterol, heart rhythm, and diabetes, and treating those risks lowers the chance of a bigger stroke later.
Symptoms depend more on where the hole is than on how big it is. A hole in a movement or speech area matches the problems people notice after the stroke. The hole itself is not active; ongoing risk comes from the blood vessels.
Sudden face droop, arm weakness, or slurred speech means calling emergency services. An old hole on a scan does not need emergency care by itself.
Head Injuries Can Leave Holes Months or Years Later
After head trauma, softened brain tissue can come from bruising with bleeding, lost blood flow, or widespread tearing of nerve fibers.11The Health Researcher’s Journal. A CASE REPORT OF 41-YEAR-OLD MALE WITH POST TRAUMATIC ENCEPHALOMALACIA This softening can develop months or even years after the injury.12The Health Researcher’s Journal. A CASE REPORT OF 41-YEAR-OLD MALE WITH POST TRAUMATIC ENCEPHALOMALACIA In infants, severe head trauma with bleeding under the skull can rarely turn large parts of both sides of the brain into many fluid-filled cysts.13Journal of Neurosciences in Rural Practice. Multicystic encephalomalacia secondary to head trauma
The damage starts at impact or soon after, but the loss of tissue is slow. A scan taken weeks or months later can therefore show changes that weren’t visible at first. Sometimes early scans simply missed a small area of damage, and the hole is the visible result of a bruise that looked minor at the time.
A hole found years later usually marks damage that has since settled. The scan only shows that tissue was lost, and it cannot say on its own which injury caused it, so doctors rely on your history and earlier scans to connect the two.
Injury holes often appear at the front and sides of the brain, which strike the inside of the skull. Holes there can match changes in mood, focus, or memory, and a report may tie them to an earlier “contusion,” meaning a brain bruise.
Mention any past concussion, fall, sports injury, or crash to the doctor, even old ones. Bring earlier scans so the doctor can compare and see the change over time. New seizures or headaches after a head injury deserve a prompt check.
Infections and Parasites That Hollow Out Tissue
A brain abscess has a dead center filled with pus, which shows up as a fluid pocket on MRI.14American Journal of Neuroradiology. MR Imaging of Brain Abscesses It is an active illness, usually with fever, headache, or new weakness, not a quiet old scar. Treatment usually means weeks of antibiotics, and larger abscesses may be drained with surgery. After healing, a small scar or hole can remain.
The larvae of the pork tapeworm can lodge in the brain as fluid-filled cysts, a condition doctors call neurocysticercosis. As the larva dies, the body’s inflammation surrounds it and the cyst fluid turns thick and cloudy.15PubMed Central. Clinical symptoms, diagnosis, and treatment of neurocysticercosis The cyst then collapses, is replaced by scar tissue, and often hardens into a small calcified spot.16PubMed Central. Clinical symptoms, diagnosis, and treatment of neurocysticercosis Some calcified spots still carry leftover inflammation.17PubMed Central. Clinical symptoms, diagnosis, and treatment of neurocysticercosis So an old calcified cyst can still trigger seizures, which is why it is often watched.
This infection is common in parts of Latin America, Asia, and Africa, and it is a leading cause of seizures where it is common. It spreads from eggs passed by a person carrying the tapeworm, often through food or hands. If you have spent time living in those regions, tell your doctor.
Some Holes Are Harmless Widened Fluid Spaces
Every brain has thin fluid channels around its blood vessels, which reports may call perivascular spaces. When one is wider than 5 mm, reports call it “dilated.”18PubMed Central. Neuroimaging of Dilated Perivascular Spaces: From Benign and Pathologic Causes to Mimics About 1.6% to 3% of healthy people have dilated spaces like these.19PubMed Central. Neuroimaging of Dilated Perivascular Spaces: From Benign and Pathologic Causes to Mimics They show up most often deep in the brain, near the top, and in the brainstem.20PubMed Central. Neuroimaging of Dilated Perivascular Spaces: From Benign and Pathologic Causes to Mimics Rarely they reach 1.5 cm or more and are called “giant” or “tumefactive” spaces, yet are still not tumors.21PubMed Central. Neuroimaging of Dilated Perivascular Spaces: From Benign and Pathologic Causes to Mimics
In follow-up scans for 6 months to over 9 years, these spaces did not change in size.22American Journal of Neuroradiology. Subcortical Cystic Lesions within the Anterior Superior Temporal Gyrus: A Newly Recognized Characteristic Location for Dilated Perivascular Spaces They match normal brain fluid on every scan type and do not light up with contrast dye.23American Journal of Neuroradiology. Subcortical Cystic Lesions within the Anterior Superior Temporal Gyrus: A Newly Recognized Characteristic Location for Dilated Perivascular Spaces
Doctors usually tell a harmless space from damage by its look, though appearance alone is not always conclusive. Harmless spaces are smooth, follow blood vessels, and have little or no scar edge. Doctors often compare with a later scan to confirm nothing changes.
If your report mentions one, ask whether it needs a repeat scan or nothing at all. Also ask whether it relates to any symptoms you have, since usually it does not.
MS Black Holes
In MS, “black holes” are spots that look dark on one type of MRI image, called T1.24PubMed. Evolution of T1 black holes in patients with multiple sclerosis imaged monthly for 4 years They can mean either temporary swelling or real loss of nerve fibers.25PubMed. Evolution of T1 black holes in patients with multiple sclerosis imaged monthly for 4 years Black holes that last are used as a sign of nerve fiber loss and disease activity.26PubMed. Black holes in multiple sclerosis: definition, evolution, and clinical correlations
Doctors track the lasting ones across scans to judge how active the MS is. More lasting holes can lead to a talk about stronger treatment, though symptoms and disability matter alongside the scan count.
Dark spots alone don’t point to MS, since small strokes can look similar. MS is diagnosed from symptoms, scan patterns over time, and other tests.
Radiation Treatment and Carbon Monoxide
Radiation damages the brain’s small blood vessels within the first 24 hours.27PubMed Central. Treatment of Radiation-Induced Brain Necrosis That injury leads to swelling, leaky vessels, and tissue death.28PubMed Central. Treatment of Radiation-Induced Brain Necrosis Even healthy brain just outside the treated area can be harmed, leading to lost blood flow, long-term inflammation, and dying tissue.29PubMed Central. Brain Radiation Necrosis Outside the Target Volume After Proton Radiation Therapy: Analyses of Multiparametric Imaging and Proton Biologic Effectiveness Someone treated for a brain tumor may later see a new hole near the treated area that is from radiation, not tumor.
The two can look alike on regular scans. Doctors use special MRI types or follow-up scans to tell them apart. Because the answer changes treatment, ask which one your team suspects.
Carbon monoxide poisoning can damage deep brain areas that control movement.30PubMed Central. Pallidoreticular damage in acute carbon monoxide poisoning: diffusion-weighted MR imaging findings It can also cause delayed damage to the white matter that appears after an early improvement.31PubMed Central. Pallidoreticular damage in acute carbon monoxide poisoning: diffusion-weighted MR imaging findings
Install carbon monoxide alarms near bedrooms, and never run engines or grills indoors. Headache, dizziness, or confusion that affects several people at home needs emergency care.
Holes Present From Birth or Caused by Genes
Bleeding in the brain before birth can leave a fluid-filled cavity present from early life (porencephaly) or a cleft through the brain (schizencephaly).32PubMed Central. Schizencephaly and Porencephaly Due to Fetal Intracranial Hemorrhage: A Report of Two Cases In one reported family, porencephaly was linked to a change in a gene called COL4A1, which affects blood vessel walls.33PubMed Central. Schizencephaly and Porencephaly Due to Fetal Intracranial Hemorrhage: A Report of Two Cases
In a rare inherited disease called vanishing white matter, MRI shows the brain’s white matter thinning out and breaking down into cysts.34PubMed. MRI Natural History of the Leukodystrophy Vanishing White Matter When it starts between ages 1 and 4, white matter can be lost quickly, leaving a severely damaged brain.35PubMed Central. Consensus-Based Expert Recommendations for Diagnosis and Clinical Management of Vanishing White Matter
Doctors may offer genetic testing when a child has unexplained cavities. A gene result can guide care and inform future pregnancies. Many children with early cavities develop seizures, weakness, or learning differences, but severity varies widely.
Delayed sitting, walking, or talking is worth raising with a pediatrician, as are weakness on one side or early hand preference. Seizures or a head that grows unusually fast should be mentioned too.
Prion Diseases Make the Brain Look Like a Sponge
Prion diseases are caused by misfolded proteins that spread through the brain. They cause widespread sponge-like damage, loss of nerve cells, scarring, and clumps of the abnormal protein.36PubMed Central. Cellular and Molecular Mechanisms of Prion Disease The tiny holes form inside nerve cells and their branches, and can be mild or severe.37PubMed Central. The intricate mechanisms of neurodegeneration in prion diseases
These holes are tiny spaces, far smaller than the pockets of fluid left by a stroke. A pathologist sees them only by examining brain tissue under a microscope, which gives the “sponge” look behind the term spongiform. A standard MRI does not show individual microscopic holes, so a scan report would not describe them as holes or cysts. The scan can show other changes, such as signal differences in certain brain regions, but those are not the holes themselves.
Prion disease causes rapidly worsening memory loss and movement problems over weeks to months. It is very rare, about 1 to 2 cases per million people each year.
What Happens After a Scan Shows a Hole
Doctors compare the hole’s look with your history, and sometimes use extra MRI types. A special MRI method that tracks water movement helps separate an abscess from a tumor with a dead center.38PubMed. Diffusion-weighted MRI features of brain abscess and cystic or necrotic brain tumors: comparison with conventional MRI Abscesses showed one clear pattern on this scan, while most tumor cysts showed the opposite.39PubMed. Differential diagnosis of intracranial ring enhancing cystic mass lesions–role of diffusion-weighted imaging (DWI) and diffusion-tensor imaging (DTI) A few tumors mimic an abscess, so the test is not perfect.40PubMed. Differential diagnosis of intracranial ring enhancing cystic mass lesions–role of diffusion-weighted imaging (DWI) and diffusion-tensor imaging (DTI)
Often the next step is a repeat scan. A hole that keeps the same size and shape over months is often old and settled, though doctors weigh this with your symptoms and history. Growth, new swelling, or contrast uptake points to something active.
Useful questions for your report: Is this old damage, a harmless space, or something active? Do you know what caused it, and does it explain my symptoms? Do I need a repeat scan, and when? Should I see a neurologist?
The hole itself is not treated; care focuses on symptoms and the cause. Seizure medicines, therapy, and controlling stroke risks help most people.