The Benign Notochordal Lesion (vs Chordoma)
- A benign intraosseous tumour arising from notochordal remnants along the path of the embryonic notochord - clivus, vertebral bodies, sacrum - and most often an incidental, asymptomatic finding.
- Imaging is the key: intraosseous, sclerotic (or mixed) on CT, marrow signal change on MRI, and no bone destruction or extraosseous soft-tissue mass.
- Chordoma is the differential that matters: lytic, destructive, a soft-tissue mass, myxoid and lobulated. Both are brachyury-positive, and BNCT may be a chordoma precursor.
- Observe the benign, asymptomatic lesion with interval imaging (0 of 16 lesions progressed at a median 21.6 months, a short follow-up; no validated interval or stopping point). Chordoma needs wide or en-bloc resection with consideration of radiotherapy.
- A provisional atypical notochordal cell tumour (benign histology, subtle cortical permeation or minimal soft-tissue extension) sits between the two; minor permeation alone should prompt specialist review rather than sacrectomy.
- “Benign notochordal cell tumour (BNCT) = benign intraosseous lesion from notochordal remnants (clivus/vertebra/sacrum); usually INCIDENTAL; INTRAOSSEOUS, SCLEROTIC, NO destruction, NO soft-tissue mass.
- “Key differential = CHORDOMA (malignant): LYTIC/destructive with an extraosseous SOFT-TISSUE MASS, myxoid/lobulated. Both notochordal + BRACHYURY-positive; BNCT may be a chordoma PRECURSOR.
- “Management: OBSERVE/surveil the benign BNCT; chordoma needs en-bloc oncological RESECTION +/- radiotherapy. Don't under-treat a chordoma or over-treat a BNCT.
Overview & Epidemiology
What it is. The benign notochordal cell tumour (BNCT) is a benign intraosseous tumour of notochordal remnant origin, arising along the path of the embryonic notochord: the clivus, the vertebral bodies and the sacrum. It sits in the notochordal tumour spectrum beside its malignant relative, chordoma, and the two share their brachyury (TBXT) marker.
How common. Notochordal rests are common autopsy findings. BNCTs have been reported in up to about 20% of spines at autopsy, a widely repeated figure for which no primary autopsy series was retrieved here, so treat it as an order of magnitude rather than a measured prevalence. The vast majority remain stable, asymptomatic and undetected; only a tiny fraction come to clinical attention, usually as an incidental finding on axial imaging.
Who. Biopsy-proven series are small, and the largest (Iorgulescu 2013) describes eight adults. There is no established sex or age predilection from cohort data; reported cases are adults.
Why it matters. The entity is a clinical problem almost entirely because of its resemblance to, and possible precursor relationship with, chordoma. Recognising it avoids the morbidity of unnecessary oncological resection, while a chordoma mislabelled as BNCT is a malignant, locally destructive tumour left to progress.
Pathophysiology: Notochordal Biology, Ecchordosis Physaliphora, and Brachyury
The notochord and its rests. The notochord is the embryonic axial midline structure. It normally regresses, and its only adult remnant is the nucleus pulposus of the intervertebral disc. Notochordal cell rests persist in the clivus, vertebral bodies and sacrococcygeal region, and BNCT, also called a giant notochordal rest or hamartoma, arises from these intraosseous rests.
The extraosseous relative. Ecchordosis physaliphora is a related benign notochordal remnant that is extraosseous and intradural, classically on the dorsal clivus in the prepontine region. It is the intracranial counterpart of the intraosseous BNCT.
Brachyury. Brachyury is the T-box transcription factor T (gene TBXT), the master regulator of notochord development, expressed in all notochordal cells: BNCT, chordoma and nucleus pulposus. Germline TBXT duplication and a common TBXT variant are chordoma susceptibility factors, which is the molecular basis of the shared marker and of the precursor link.
The precursor question. BNCT may be a precursor to chordoma. Most BNCTs remain stable, and only a small proportion behave as precursors, with some chordomas arising adjacent to a BNCT.
Clinical Presentation
The usual story. BNCT is characteristically asymptomatic and incidental, found on CT or MRI performed for unrelated reasons. When patients do present, the reported context is non-specific back or axial pain that prompts imaging; every patient in the Iorgulescu series presented this way. The lesion is then incidental to the symptom rather than the proven pain generator, so "incidental" describes how the lesion relates to the pain, not a screening discovery.
Red flags. These point away from BNCT and toward chordoma:
- Progressive or night pain
- Neurological symptoms: radiculopathy, sacral plexus symptoms, bladder or bowel disturbance
- A palpable presacral mass on rectal examination
- Any imaging evidence of cortical destruction or a soft-tissue component
Symptoms do not decide it. Symptoms favour chordoma, but alone they do not separate the two. The Terzi cases all presented with subacute mild pain, including the one that harboured incipient chordoma; the imaging assessment of aggressiveness is what makes the call.
Examination. Usually normal in BNCT. Any neurological finding or palpable mass should be treated as chordoma until proved otherwise and referred to a specialist spine/tumour centre.
Imaging and the Chordoma Distinction
What decides it. The two tumours share an origin and a marker and can be difficult to distinguish, so the radiological assessment of aggressiveness is central. Bone destruction and an extraosseous soft-tissue mass are the discriminators: BNCT has neither, and their presence favours chordoma.
BNCT on CT. A well-defined intraosseous focus of sclerosis (or mixed sclerosis), with no cortical destruction, no periosteal reaction and no soft-tissue mass.
BNCT on MRI. Low signal on T1, replacing the normal fatty marrow, and high signal on T2. The key discriminator on MRI is little or no contrast enhancement; chordoma enhances heterogeneously.

- Benign notochordal cell tumour
- Benign (often incidental)
- Chordoma
- Malignant
- Benign notochordal cell tumour
- Intraosseous, sclerotic, NO destruction
- Chordoma
- Lytic, destructive
- Benign notochordal cell tumour
- Absent
- Chordoma
- Present (extraosseous)
- Benign notochordal cell tumour
- Sheets of bland vacuolated cells; no myxoid lobules
- Chordoma
- Myxoid/lobulated; physaliphorous cells
- Benign notochordal cell tumour
- Notochordal; brachyury+
- Chordoma
- Notochordal; brachyury+
- Benign notochordal cell tumour
- Observation/surveillance
- Chordoma
- En-bloc resection +/- radiotherapy



The non-chordoma differential. Other sclerotic or marrow lesions separate on their own features:
- Bone island (enostosis): dense homogeneous sclerosis with radiating "thorny" margins that blend into the trabeculae, and low on all MRI sequences, without the marrow-replacing T2-high signal
- Vertebral haemangioma: "corduroy" or "polka-dot" pattern, fat-containing (T1-high), and enhances
- Sclerotic metastasis: older patient, known primary, often multiple; may destroy cortex, enhance or be PET-avid
Histology
The benign pattern. BNCT consists of sheets of bland, adipocyte-like vacuolated notochordal cells filling the marrow space. It lacks the myxoid or chondroid matrix, the lobular architecture and the bone destruction of chordoma.
Immunohistochemistry. Brachyury, S100, EMA and cytokeratin confirm notochordal differentiation, but they do not by themselves separate BNCT from chordoma.

The Grey Zone: When the Lesion Is Neither Clearly Benign Nor Clearly Chordoma
Treating destruction and soft-tissue extension as an absolute switch between observation and en-bloc surgery is clean but incomplete. A proposed intermediate group exists, and knowing it is what separates a safe answer from a confident one.
Atypical notochordal cell tumour. Carter and colleagues described four adults, aged 53 to 83, with lumbar or sacral notochordal tumours that fitted neither the BNCT nor the chordoma criteria. Three showed subtle cortical permeation with minimal soft-tissue extension on imaging, yet all four had the histology of a benign notochordal cell tumour, two with focal myxoid change.
How they behaved. Three were followed with serial imaging for 26 to 120 months: two showed no progression, and one grew 3.7 mm over ten years. The pathologists proposed the provisional label atypical notochordal cell tumour for lesions failing the criteria for either diagnosis, arguing that calling them chordoma "precipitates potentially overly aggressive surgical management". With four patients it remains a proposal rather than an established category.
Enhancement can mean real chordoma. The grey zone cuts both ways. In Terzi's three-case series the two classic lesions were observed without progression, while the third, with an atypical lytic pattern and contrast enhancement, underwent en-bloc resection with significant associated morbidity, and the specimen contained coexistent foci of incipient chordoma. An enhancing or lytic notochordal lesion is not over-called when it is treated seriously: the price of getting it wrong is a missed malignancy in one direction and a sacrectomy in the other.
Know the three-way, not the two-way: benign notochordal cell tumour (intraosseous, sclerotic, no destruction, observe), chordoma (lytic, destructive, soft-tissue mass, enhances - resect), and the proposed atypical notochordal cell tumour in between (benign histology with subtle cortical permeation, followed rather than resected in three of the four reported cases).
Management
Observe the benign lesion. A benign, asymptomatic BNCT is managed by observation with interval imaging to confirm stability. The support is the largest biopsy-proven series: 16 lesions in 8 patients followed radiographically for a median of 21.6 months (range 8.5 to 71.2), none of which progressed radiographically or symptomatically. The authors state plainly that their conclusion is limited by that short follow-up.
No validated schedule. No validated surveillance interval, imaging modality or stopping point exists. Published follow-up ranges from under a year to ten years and no schedule has been tested, so interval imaging is a reasonable practice justified by the natural history observed so far, not a protocol, and should be set with the specialist centre.
The atypical lesion. Benign histology with subtle cortical permeation or minimal soft-tissue extension, the provisional atypical notochordal cell tumour, was followed rather than resected in three of the four reported cases. Minor permeation alone should prompt specialist review, not a sacrectomy.
Resect the chordoma. Chordoma requires wide or en-bloc oncological resection, with consideration of adjuvant radiotherapy (e.g. proton therapy).
A genuine BNCT is watched and spared surgery; a chordoma undergoes major oncological resection. The two share an origin and a marker, yet their management could hardly be more different, and the error in either direction is serious. Biopsy and management of equivocal axial notochordal lesions belong at a specialist spine/tumour centre.
Complications & Prognosis
The lesion itself. In the available follow-up, biopsy-proven BNCTs do not progress (Iorgulescu 2013), and the atypical-category cases followed were similarly indolent (Carter 2017). The prognosis of a genuine BNCT is therefore excellent.
Transformation or coexistence with chordoma. This is the complication that matters. The Terzi case proves an atypical notochordal lesion can harbour incipient chordoma, but no series provides a rate: the cohorts are too small and too short to quantify transformation risk, which is precisely why surveillance has no validated stopping point.
The iatrogenic complications. En-bloc sacral or spinal resection carries significant morbidity, as the Terzi resected case illustrates: sacral nerve sacrifice, bladder, bowel and sexual dysfunction, and wound and reconstruction problems. Over-calling a BNCT as chordoma inflicts that morbidity for a lesion that would never have harmed the patient. Both error directions are complications of the diagnosis, and both are minimised by specialist-centre review.
Surveillance as the safety net. Interval imaging is both the management and the safety net: it confirms stability, and it catches the rare lesion that declares itself aggressive early enough for curative resection.
Mnemonics & Memory Aids
NOTOCHORD
Hook:NOTOCHORD: Notochordal axial, Often incidental, no exTraosseous mass, nO destruction, CHordoma differential, Origin shared (brachyury), Resect chordoma, Don't over-treat BNCT.
BEDSFeatures That Favour Chordoma
Hook:Chordoma BEDS the patient: Brachyury+ (both), Enhances, Destructive, Soft-tissue mass.
RESTBNCT Biology
Hook:A BNCT is a notochordal REST: Remnant origin, Ecchordosis relative, Sclerotic/contained, TBXT (brachyury) positive.
Clinical Decision Scenarios
Practise clinical reasoning and management decisions out loud
“An incidental sclerotic intraosseous lesion is found in a sacral vertebra. How do you decide whether it is a benign notochordal cell tumour or a chordoma?”
What it is
- Benign intraosseous lesion from notochordal remnants (clivus/vertebra/sacrum)
- Usually incidental and asymptomatic
- Histology: sheets of bland vacuolated notochordal cells filling marrow
Imaging (benign hallmarks)
- Intraosseous, sclerotic (CT), marrow signal change (MRI)
- NO bone destruction; NO extraosseous soft-tissue mass
- Non-aggressive, contained appearance
vs Chordoma
- Chordoma: lytic/destructive + extraosseous soft-tissue mass, myxoid/lobulated
- Both brachyury-positive; BNCT may be a chordoma precursor
- Destruction/soft-tissue mass favours chordoma
Management
- BNCT (asymptomatic): observation + imaging surveillance
- Chordoma: en-bloc oncological resection +/- radiotherapy (proton)
- Equivocal/aggressive axial lesions → specialist spine/tumour centre
Evidence & Key Studies
Sacral tumors: imaging, diagnostic challenges and tumor mimics (notochordal lesions)
- Primary tumours of the sacrum/spine can arise from notochordal remnants, with chordoma recognised for its propensity to occur in the sacrum; imaging is essential in diagnosis, pretreatment evaluation and assessing treatment response.
- Many entities have characteristic clinical, epidemiological and imaging findings that allow a confident diagnosis or a narrow differential, enabling a systematic approach to sacral/axial masses.
- A definitive diagnosis is not always achievable on imaging alone, as some lesions lack specific features - relevant to distinguishing benign notochordal lesions from chordoma.
The origin of axial/sacral tumours from notochordal remnants, the propensity of chordoma for the sacrum, the central role of imaging in diagnosis and pretreatment evaluation, and the fact that imaging alone is not always definitive (relevant to the benign-notochordal-lesion versus chordoma distinction) come from the cited Adin sacral-tumours review. The specific imaging hallmarks of benign notochordal cell tumour (intraosseous, sclerotic, no destruction/soft-tissue mass), the shared brachyury-positive notochordal origin with chordoma, the precursor relationship, and the observation-versus-resection management are standard, well-established teaching. The natural-history figures - 16 lesions in 8 patients, median follow-up 21.6 months, no progression - come from the cited Iorgulescu series, a single retrospective centre whose authors state the short follow-up as a limitation. The atypical notochordal cell tumour category, its imaging and the ten-year 3.7 mm growth come from the cited Carter series of four patients and remain a provisional designation rather than a WHO entity. The observation that an enhancing, lytic notochordal lesion resected with significant morbidity contained incipient chordoma is from Terzi and colleagues (Spine 2012, PMID 22772575), a three-case series. No validated surveillance interval, imaging modality or stopping point for a benign notochordal cell tumour was retrieved, and no cohort large enough to quantify the risk of transformation exists - so the schedule should be set with the treating specialist centre rather than from a published protocol. The figure that notochordal rests are found in up to about 20 percent of spines at autopsy is widely repeated in the literature; no primary autopsy series supporting that exact proportion was retrieved here, so it is given as an order of magnitude. See also chordoma; the library has no dedicated sacral-tumour or spinal-bone-tumour topic, and the sacral lesions most often confused with these on imaging are covered in sacral insufficiency fracture.