What does not show up on a CT scan?

A CT (computed tomography) scan is a type of X-ray that produces cross-sectional images of the body using X-rays and a computer. It provides more detailed information than a standard X-ray. CT scans are used to diagnose and monitor a wide range of conditions affecting the head, chest, abdomen, pelvis, spine, brain, and other parts of the body. They allow doctors to see inside the body without having to perform invasive surgery. However, there are some limitations to what will be visible on a CT scan. Not everything will show up.

Soft Tissues

One of the main limitations of CT scans is that they do not show soft tissues very clearly. Soft tissues include muscles, tendons, ligaments, fascia, nerves, fibrous tissues, fat, skin, and blood vessels. On a CT scan, soft tissues often look grainy and indistinct compared to denser structures like bone. This makes it difficult for doctors to identify abnormalities or diseases affecting primarily soft tissues using CT scans alone.

For example, cancerous tumors in soft tissues like the pancreas or liver may be difficult to detect on a CT scan. Herniated disks or torn ligaments in the spine can also be challenging to diagnose definitively. Doctors would need an MRI scan in addition to CT to get a clearer picture of soft tissue structures. MRIs use strong magnetic fields rather than X-rays to generate images. The MRI creates better contrast between the soft tissues.

Bone Marrow Issues

Bone marrow is the soft, fatty tissue inside bones that produces new blood cells. It contains stem cells that can develop into red blood cells, white blood cells, and platelets. Diseases of the bone marrow like leukemia, myeloma, aplastic anemia, and bone marrow metastases may not show up well on CT scans.

In healthy individuals, bone marrow has a uniform fatty composition that appears dark on CT scans. Problems like decreased blood cell production, cancerous myeloma cells, or metastatic cancer would structurally alter the bone marrow, but these changes are often subtle and can be missed. Doctors would need to do bone marrow sampling and biopsy to definitively diagnose most bone marrow diseases.

Very Small Structures

While CT scan images provide excellent anatomic detail, the resolution does have limits. Tiny structures smaller than 1-2 millimeters are difficult to visualize on CT scans. Important structures that may not be seen well include small arterial blockages, tiny endocrine tumors, small inner ear structures, very small fractures, and narrow sinus cavities.

Doctors would need MRI or ultrasounds, which have higher resolution, to properly evaluate these small structures. Contrast dye is often used to highlight blood vessels and improve visualization of small blockages as well. But ultimately CT lacks the fine detail needed for diagnosis of the tiniest structures and pathologies.


Hernias occur when an organ or fatty tissue protrudes through a weak spot or tear in the surrounding muscle or connective tissue. Types of hernias include inguinal, femoral, incisional, umbilical, and hiatal hernias. Unfortunately, hernias often do not show up on CT scans even when present.

Unless the hernia is obstructed or inflamed when the CT is done, the abnormal protrusion may be difficult to appreciate. Even large hernias can be missed on CT if the radiologist is not specifically looking in the area of suspected pathology. Physical exams and ultrasounds are more accurate for diagnosing uncomplicated hernias. Follow up MRI can also be useful after initial diagnosis by exam.

Early Arthritis

Arthritis involves inflammation and gradual deterioration of the joints. Osteoarthritis is caused by age-related wear and tear, while rheumatoid arthritis results from the immune system attacking the joints. In early stage arthritis, damage is confined to soft tissues like ligaments, tendons, and cartilage. Bone changes occur later.

Since CT scans do not show soft tissues well, radiologists can miss early arthritis on these X-rays before bones are affected. Rheumatoid arthritis also begins as joint inflammation prior to bony changes. MRI scans and ultrasounds are better for viewing soft tissue joint structures and identifying early arthritis.

GI Issues

CT scans are not the optimal imaging choice for diagnosing most gastrointestinal issues. They do not provide the contrast resolution needed to properly evaluate the digestive organs and bowel. CT scans are used for assessing acute abdominal emergencies like appendicitis, bowel obstruction, diverticulitis, and pancreatitis. However, for more routine diagnosis of conditions like ulcers, inflammatory bowel diseases, hernias, and polyps, MRIs, ultrasounds, and endoscopies are superior. CT is also not ideal for picking up subtle GI bleeding sources.

Partial Tears of Tendons and Ligaments

Tendons connect muscle to bone, while ligaments connect bones to other bones at joints. Partial tears of major tendons and ligaments may not be visible on CT scans. Since CT does not delineate soft tissues well, small partial tears are often not appreciable. MRI gives the detailed soft tissue imagery required to pick up these partial tears affecting tendons and ligaments.

For example, partial ACL knee ligament tears and partial rotator cuff tendon tears in the shoulder can easily be missed on CT but would be detected on MRI. If physical exam and symptoms suggest a partial tear, MRI would be warranted even if CT is negative.

Low-Grade or Early Stage Cancers

CT scans may miss early stage or low-grade cancers in certain parts of the body, especially where soft tissue contrast resolution is critical. For example, early stage cancers of the kidney, uterus, ovary, pancreas, and liver may not show up well on CTs until they grow larger or spread. Low grade prostate and bladder cancers can also be difficult to detect on CT.

MRI provides superior soft tissue detail and is more likely to catch small or early stage cancers. But MRI availability is more limited. CT remains the mainstay for routine cancer screening and initial workup. But MRI, PET scans, and tissue sampling are often needed to confirm early cancers when clinical suspicion is high despite negative CTs.

Brain Abnormalities

CT scans are often used as initial imaging tests for brain pathology like tumors, bleeding, strokes, and concussions. But MRI brain scans are superior for detecting smaller and subtler brain abnormalities. MRI picks up more small infarcts, low grade gliomas, mild microbleeds, white matter demyelination, early MS plaques, and microscopic petechial hemorrhages.

Headaches and neurological symptoms with a normal CT of the brain often warrant follow up MRI scanning to search for underlying pathology. CT is good for ruling out large obvious brain lesions, but MRI is needed to identify more subtle brain abnormalities.

Hairline Fractures

Since CT does not provide clear visualization of very tiny structures, hairline fractures are sometimes missed on CT scans. Undisplaced or nondisplaced fractures where the bone fragments maintain alignment can be difficult to appreciate on CT, especially without contrast dye. MRI is the optimal choice for diagnosing most hairline fractures.

In areas like ribs, skull, sacrum, and metatarsals and metacarpals, follow up MRI scanning would be prudent after a negative CT scan if clinical suspicion for a fracture persists based on history and physical exam. Comparison xray views over time also assist in identifying hairline fractures eventually as callous formation occurs during the healing process.

Foreign Bodies

While metal foreign bodies like bullets are usually well seen on CTs, smaller plastic or wood foreign bodies can be challenging to identify. Radiolucent plastic, wood splinters, small glass fragments, and fish bones may not stand out within surrounding soft tissues on CT scans. Ultrasounds and MRI provide better foreign body detection due to superior soft tissue resolution.

In the setting of skin lacerations, injection drug use, or penetrating trauma, negative CT scan does not fully exclude a retained foreign body. MRI, ultrasound, and surgical exploration may be needed for definitive diagnosis if symptoms persist.

Meniscal Tears in the Knees

The meniscus is a C-shaped fibrocartilage disk that provides cushioning between the thigh and shin bones. Meniscal tears are a common cause of knee pain and loose body sensation. Unfortunately, MRI is superior to CT for identifying meniscal tears. Unless the tear is large enough to displace meniscal fragments, it may not be visible on CT. Radiologists prefer MRI for evaluating knee soft tissue structures including the menisci. CT arthrogram with contrast dye injection may allow better delineation of some meniscal tears.

Muscle Strains and Tears

Strains or tears of smaller muscle groups like the rotator cuff and hamstrings are challenging to diagnose on CT due to limitations is soft tissue contrast. Muscles often appear normal on CT despite grade 1 or 2 sprains and strains. MRI gives exquisite muscle detail to detect partial muscle tears, localized edema, and hemorrhage that occurs with muscle strains. In high performance athletes requiring return to play decisions, MRI allows radiologists to distinguish between grade 1, 2, and 3 muscle strains. CT cannot characterize muscle injuries with the same degree of accuracy.

Inner Ear Disorders

The inner ear houses the cochlea for hearing and vestibular semicircular canals for balance. Disorders of the inner ear structures can cause dizziness, hearing loss, and ringing sensations but usually require MRI for accurate diagnosis. The fine anatomic detail of the membranous labyrinth including nerves like the cochlear, vestibular, and facial nerves is visualized optimally via MRI as CT has limited resolution. Conditions like acoustic neuromas, labyrinthitis, and Ménière’s disease cannot be diagnosed definitively by CT alone.

Inflammatory Bowel Diseases

Crohn’s disease and ulcerative colitis fall under the umbrella of inflammatory bowel diseases. They cause chronic gastrointestinal symptoms like diarrhea, abdominal pain, and bloody stools. CT enterography is sometimes performed in suspected inflammatory bowel disease, but it may miss earlier stages and underestimate the extent of disease. Compared to CT, MRI enterography better characterizes the mucosal changes of active inflammatory bowel disease. MRIs also do not use ionizing radiation, an advantage for patients who need frequent monitoring.

Table Summary of What Does Not Show Well on CT Scans

Type of Pathology Examples
Soft Tissue Abnormalities Early tumors, small muscle tears, tendonitis, nerve inflammation
Subtle Bone Marrow Changes Leukemia, myeloma, metastatic cancer, aplastic anemia
Very Small Structures Tiny fractures, arterial blockages, inner ear structures
Partial Ligament and Tendon Tears Partial ACL tear, partial rotator cuff tear
Low Grade or Early Stage Cancers Prostate, bladder, uterine, pancreatic, renal cancers
Brain Abnormalities Small infarcts, low grade tumors, white matter lesions, early MS plaques
Hairline Fractures Skull, ribs, sacrum, metatarsal/metacarpal fractures
Small Foreign Bodies Plastic, wood splinters, glass fragments
Meniscal Tears Knee meniscal tears
Muscle Strains Grade 1-2 rotator cuff strains, hamstring strains
Inner Ear Disorders Acoustic neuromas, Ménière’s disease, labyrinthitis
Inflammatory Bowel Diseases Crohn’s disease, ulcerative colitis


In summary, CT scans have revolutionized medical imaging and diagnosis due to their detailed cross-sectional views of anatomy. However, they do have limitations in detecting abnormalities primarily affecting soft tissues, small structures, bones marrow, and the inner ear. MRI and ultrasound provide complementary information and often detect pathology initially missed on CTs. Knowledge of the advantages and disadvantages of CT helps ensure the appropriate use of multi-modality imaging options for accurate diagnosis and treatment planning.

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