Basaloid Squamous Cell Carcinoma of the Larynx: Understanding Your Pathology Report

Section Editor: Jason Wasserman MD PhD FRCPC
July 27, 2026

Basaloid squamous cell carcinoma is an uncommon type of squamous cell carcinoma of the larynx, the voice box. It starts in squamous cells, the flat cells that line the inside of the larynx, and it is named for the way most of its cells look under the microscope. Instead of the larger cells seen in ordinary squamous cell carcinoma, most of the cells are small, dark, and tightly packed, resembling the basal cells found at the bottom of the normal lining. Pathologists describe this appearance as basaloid.

A feature of this tumor is that it has two parts. Alongside the basaloid areas, there is usually an area that looks like ordinary squamous cell carcinoma. Finding both components together is what establishes the diagnosis, and it confirms that this is a type of squamous cell carcinoma rather than a different kind of cancer.

In the larynx, basaloid squamous cell carcinoma arises most often in the supraglottis, the part of the voice box above the vocal cords. Compared with ordinary squamous cell carcinoma of the larynx, it is more often found at a later stage and reaches the lymph nodes in the neck more frequently, which is why it is treated with particular care.

This article explains the findings you are likely to see on a pathology report for basaloid squamous cell carcinoma of the larynx, what each one means, and why it matters for your care.

What causes basaloid squamous cell carcinoma of the larynx?

Basaloid squamous cell carcinoma of the larynx develops for the same reasons as ordinary squamous cell carcinoma. The squamous cells lining the larynx are damaged repeatedly over many years, and each round of damage and repair leaves small errors in the cells’ genetic material. Once enough errors accumulate, the cells grow without normal control. The main causes are:

Tobacco. The most important risk factor, in any form.
Alcohol. Heavy use raises risk on its own, and combining it with smoking raises risk considerably more than either alone.
Previous radiation to the neck. Radiation given years earlier for another condition can raise the risk of a cancer developing in the treated area.
A weakened immune system. This includes long-term immune suppression after an organ transplant.

In the throat behind the mouth, some basaloid squamous cell carcinomas are caused by human papillomavirus (HPV) and behave more favorably. In the larynx, this is uncommon, and most of these tumors are not related to HPV. Your report may still include HPV or p16 testing to establish this.

What are the symptoms of basaloid squamous cell carcinoma of the larynx?

The symptoms of basaloid squamous cell carcinoma of the larynx depend on where in the voice box the tumor started and how far it has grown. Because most arise in the supraglottis, above the vocal cords, hoarseness may appear later than it would with a tumor on the vocal cords themselves. Common symptoms include:

A lump in the neck, which may mean the cancer has spread to a lymph node, and is sometimes the first sign
A sore throat or a feeling of something in the throat that does not go away
Difficulty or pain with swallowing
Hoarseness or a change in the voice
Ear pain on one side that is not caused by an ear infection
Noisy breathing or shortness of breath if the tumor narrows the airway
Unexplained weight loss

Because tumors above the vocal cords can grow before affecting the voice, symptoms such as a persistent sore throat or a neck lump should be assessed by an ear, nose, and throat specialist rather than waiting for hoarseness to develop.

How is the diagnosis made?

The diagnosis is made when a pathologist examines a tissue sample under the microscope. The sample is obtained by biopsy during a procedure called microlaryngoscopy, in which a thin scope is passed through the mouth under general anesthetic so the surgeon can see the larynx directly and take samples.

Under the microscope, the tumor grows in nests and cords of small, dark, closely packed cells. The centers of these nests often contain necrosis, an area of dead tumor cells, and this is a characteristic feature rather than a sign that something has gone wrong. Mitotic figures, cells caught in the act of dividing, are usually numerous. Alongside these basaloid areas, the pathologist looks for a squamous component, which may be an area of ordinary squamous cell carcinoma or an abnormal area confined to the surface lining.

One practical point is worth knowing. A small biopsy may sample only part of the tumor, and if it captures only the ordinary squamous areas, the first report may describe a conventional squamous cell carcinoma. The basaloid nature sometimes becomes apparent only when the whole tumor is examined after surgery. If your diagnosis appeared to change between the biopsy report and the final report, this is a common reason and does not mean an error was made.

Because the basaloid appearance can resemble other tumors that occur in the same area, additional testing called immunohistochemistry is routinely performed. Those results are described in the next section. Once the diagnosis is confirmed, imaging such as a CT scan, MRI, or PET-CT shows how far the tumor extends and whether lymph nodes are involved.

Immunohistochemistry

Immunohistochemistry uses antibodies to detect specific proteins in the tumor cells. For this diagnosis, it serves a specific purpose: small, dark, tightly packed cells can look similar in several very different cancers, and these tests establish which one is present. That matters because the alternatives are treated differently. The results appear on your pathology report as a list of markers, each reported as positive or negative. The markers most often used are:

p63 and p40: positive. Markers of squamous cells found in the nucleus. In basaloid squamous cell carcinoma, they are positive throughout the tumor. This widespread pattern helps separate it from adenoid cystic carcinoma, a salivary gland cancer that can look similar but stains only in part of each tumor nest.
Cytokeratins: positive. Your report may name specific ones, such as pancytokeratin or CK5/6. These are proteins found in cells that form linings, and a positive result confirms the tumor arises from the lining of the larynx.
Synaptophysin, chromogranin, and INSM1: negative. These are markers of neuroendocrine cells. A negative result helps rule out a neuroendocrine tumor or small cell carcinoma, which can look similar under the microscope but are treated quite differently.
p16: usually negative. p16 is used as a stand-in marker for HPV infection. In the larynx, these tumors are usually not caused by HPV, so a negative result is expected. A positive result would prompt further testing for the virus.

Not every case needs every marker, so a report listing only some of them is not incomplete. Taken together with the appearance of the tumor and the presence of a squamous component, these results confirm basaloid squamous cell carcinoma rather than one of the tumors it can resemble.

Is basaloid squamous cell carcinoma given a histologic grade?

Usually not in the same way as ordinary squamous cell carcinoma. Basaloid squamous cell carcinoma is not typically assigned a grade of well, moderately, or poorly differentiated, because this subtype is regarded as high grade by its nature. The small, dark, rapidly dividing cells that define it already indicate a high degree of abnormality.

Your report may state directly that the tumor is high grade, or it may simply name the subtype without giving a grade. If you are looking for a well, moderate, or poor grade and cannot find one, nothing has been left out.

Tumor extension into nearby structures

Your report will describe how far the cancer has grown from where it started. Basaloid squamous cell carcinoma begins in the lining of the larynx and can grow into the deeper layers of the laryngeal wall, into the cartilage that forms the framework of the voice box, or beyond the larynx into the thyroid gland, the windpipe, the esophagus, or the soft tissues of the neck.

Growth through cartilage or beyond the larynx raises the tumor stage and generally means a larger operation. Your report or your surgeon will also describe whether the vocal cords still move normally. A vocal cord that has stopped moving, described as fixed, indicates the tumor has grown into the muscles that move it, and this raises the stage even when the cartilage is not involved.

Perineural invasion

Perineural invasion means cancer cells are growing along or around a nerve. Nerves provide a path that cancer cells can follow beyond the visible edge of the tumor. Your report will state whether perineural invasion is present or absent. When present, it is associated with a higher chance of the cancer returning at the original site, and it is one of the findings the treatment team weighs when considering radiation after surgery.

Lymphovascular invasion

Lymphovascular invasion means cancer cells have entered a small blood vessel or lymphatic channel near the tumor. These vessels can carry cancer cells to the lymph nodes or, less often, to distant organs. Your report will state whether it is present or absent. It is found relatively often in this subtype and points to a higher chance that cancer cells have spread beyond the tumor.

Surgical margins

Margins are the cut edges of the tissue removed during surgery. The pathologist inks these edges and examines how close the tumor comes to each one.

Negative (clear) margin. No cancer cells at the inked edge. This suggests the tumor was removed completely.
Close margin. Cancer cells come within a few millimeters of the edge without reaching it. This raises the chance of the cancer returning at the same site.
Positive (involved) margin. Cancer reaches the inked edge, meaning some may remain. This is one of the main reasons the treatment team considers further surgery or radiation.

Margins in the larynx are reported separately by location: the mucosal margins at the surface lining, the deep soft tissue margin, and, when cartilage has been removed, the cartilage margin.

Lymph nodes

Lymph nodes are small immune organs that filter fluid draining from the tissues. Basaloid squamous cell carcinoma reaches the lymph nodes in the neck more often than ordinary squamous cell carcinoma of the larynx, and it frequently does so early, so a neck dissection to remove a group of these nodes is usually performed as part of surgery. The pathologist examines each node and reports:

How many lymph nodes were examined and how many contained cancer. Usually written as a ratio, such as 3 of 28. The risk of the cancer returning rises with the number of involved nodes.
The size of the largest deposit of cancer. Measured in millimeters.
Extranodal extension. This means cancer cells have broken through the outer capsule of a lymph node into the surrounding tissue. It is one of the most important adverse findings on the report and is among the findings most likely to lead the treatment team to recommend chemotherapy given together with radiation after surgery.

If no cancer is found in any lymph node, your report will say so. This is a favorable finding.

PD-L1

PD-L1 is a protein that some cancer cells display on their surface to avoid being attacked by the immune system. Immunotherapy drugs called checkpoint inhibitors, such as pembrolizumab (Keytruda) and nivolumab (Opdivo), block this signal so the immune system can recognize and attack the cancer.

PD-L1 testing is not needed to make the diagnosis. It is generally performed when the cancer cannot be removed by surgery, has returned after treatment, or has spread to distant parts of the body. The result is reported as a Combined Positive Score, or CPS, a number that reflects how many cells in and around the tumor show PD-L1. A CPS of less than 1 is considered negative. A CPS of 1 or higher is considered positive and means immunotherapy may be an option, and a higher score suggests the cancer is more likely to respond. Your report will give the specific number. You can read more in the article on PD-L1 testing in cancer.

Pathologic stage (pTNM)

The pathologic stage describes how far the cancer has spread, based on the tissue examined under the microscope. It uses the TNM system, which has three parts: T for the size and extent of the primary tumor, N for spread to the lymph nodes in the neck, and M for spread (metastasis) to more distant parts of the body. The letter “p” in front, as in pT and pN, means the stage was determined by examining tissue rather than by imaging alone. Basaloid squamous cell carcinoma is staged using the same system as ordinary squamous cell carcinoma of the larynx.

Tumor stage (pT)

The exact criteria for the T category depend on which part of the larynx the cancer started in, because each region has different boundaries. The general pattern is the same across all three, based on how far the tumor has spread within and beyond the larynx and whether the vocal cords still move.

pT1. Tumor confined to one part of the larynx, with the vocal cords moving normally.
pT2. Tumor has extended into a neighboring part of the larynx or an adjacent area, or vocal cord movement is reduced.
pT3. Tumor is still confined to the larynx but a vocal cord has stopped moving, or the tumor has grown into certain deeper spaces or the inner surface of the thyroid cartilage.
pT4a. Tumor has grown through the cartilage or beyond the larynx into nearby structures such as the windpipe, the thyroid gland, the esophagus, or the soft tissues of the neck.
pT4b. Tumor has grown into deeper structures such as the space in front of the spine, or surrounds the carotid artery. These tumors usually cannot be removed completely by surgery.

Nodal stage (pN)

pN0. No cancer found in any lymph node.
pN1. Cancer in a single lymph node on the same side as the tumor, 3 cm or smaller, without extranodal extension.
pN2. Cancer in a larger node, in more than one node, or in nodes on both sides of the neck, in ways set out by the staging system. This category also includes a single small node on the same side that shows extranodal extension.
pN3. Cancer in a node larger than 6 cm, or extranodal extension in any node beyond the situation covered by pN2.

Your report may not include the M category, because spread to distant parts of the body is usually determined by imaging rather than by the pathologist. Your treatment team combines the pathology findings with your scans to arrive at the overall stage. You can read more in the article on TNM staging.

What is the prognosis for basaloid squamous cell carcinoma of the larynx?

Prognosis means the likely course and outcome of a disease. For basaloid squamous cell carcinoma of the larynx, two things are consistent across published studies: this subtype is more often found at an advanced stage than ordinary squamous cell carcinoma, and it reaches the lymph nodes in the neck more frequently.

Whether it carries a worse outlook than ordinary squamous cell carcinoma at the same stage is less settled. The largest study of laryngeal cases found worse survival for this subtype regardless of stage, location, or treatment. Other studies that matched patients by site, stage, and treatment found survival and recurrence rates similar to ordinary squamous cell carcinoma, and suggested that much of the difference in overall outcome reflects the later stage at which these tumors are found rather than the tumor type itself. Because this subtype is uncommon, most studies involve small numbers of patients, which is part of why the picture remains mixed.

In practice, this means that the stage of your cancer and the specific findings on your report matter more than the subtype alone. The findings associated with a higher risk of the cancer returning are:

Extranodal extension. One of the strongest adverse findings, and a common reason for adding chemotherapy to radiation after surgery.
Positive or close margins. Associated with a higher chance of the cancer returning at the original site.
Multiple involved lymph nodes. Risk rises with each additional node containing cancer.
Tumor growth beyond the larynx. Reflects more extensive disease.
Perineural or lymphovascular invasion. Both point to a higher chance of the cancer returning or spreading.

One factor is within your control. Continuing to smoke after treatment is associated with higher rates of the cancer returning and with a greater risk of a second, separate cancer developing in the head, neck, or lungs. Support for stopping tobacco is a standard part of care and worth asking for.

What happens after the diagnosis?

After the diagnosis is confirmed, your pathology report is reviewed together with your imaging and overall health, usually by a team that includes ear, nose, and throat surgeons, radiation oncologists, medical oncologists, and pathologists. The report does not decide treatment on its own, but several of its findings shape the options the team will discuss with you.

Treatment usually combines more than one approach. Surgery to remove the tumor, together with removal of lymph nodes in the neck, is common for tumors that can be completely removed, and depending on the size and location, this may mean removing part of the larynx or, in some cases, the whole larynx in an operation called a total laryngectomy, which permanently changes how you breathe and speak. Because this subtype is found at a later stage and reaches lymph nodes more often, radiation after surgery is frequently discussed, and chemotherapy given together with radiation may be considered when the report shows findings such as positive margins, extranodal extension, or several involved lymph nodes. For some tumors, radiation with chemotherapy may be offered instead of surgery with the aim of preserving the larynx. For cancer that has returned or spread, options include chemotherapy, the targeted drug cetuximab, and immunotherapy. Because this subtype is uncommon, clinical trials are worth asking about.

Supportive care is a central part of treatment because the larynx is essential to breathing, swallowing, and speech. Speech and swallowing therapy, nutrition support, and a dental assessment before radiation are all standard. If a total laryngectomy is needed, a speech-language pathologist will work with you on the options for producing speech afterward. Follow-up involves regular examination of the larynx and neck along with imaging, most intensively in the first two to three years.

Questions to ask your doctor

Was the diagnosis confirmed by immunohistochemistry, and were other tumor types ruled out?
Did my biopsy report and my final report give the same diagnosis, and if not, why?
Which part of my larynx did the cancer start in?
Did the tumor grow into cartilage or beyond the larynx?
Do my vocal cords still move normally?
Were the surgical margins clear?
Was perineural or lymphovascular invasion found?
How many lymph nodes were removed, and how many contained cancer?
Was extranodal extension present?
What are my pT and pN categories, and what is my overall stage?
Was HPV or p16 testing performed, and what did it show?
Was PD-L1 testing done, and what was the CPS result?
Does the basaloid subtype change my treatment compared with ordinary squamous cell carcinoma?
What are my treatment options, and is preserving my voice possible?
How often will I be followed, and for how long?