Squamous carcinoma in situ of the larynx

What is squamous carcinoma in situ (CIS) of the larynx?

Squamous carcinoma in situ (CIS) is a non-invasive type of laryngeal (throat) cancer. Squamous carcinoma in situ starts from the squamous cells that cover the inner surface of the larynx. Squamous carcinoma in situ can start in any part of the larynx although the most common location is the vocal cord. If left untreated, squamous carcinoma in situ almost always turns into a type of invasive cancer called squamous cell carcinoma. Another name for squamous carcinoma in situ is severe squamous dysplasia.

The larynx

When we breathe, air travels from our mouth and nose to our lungs. On its way to the lungs, air passes through a part of the throat called the larynx. You cannot see your larynx because it starts at the very back of the tongue.

Most of the larynx is a hollow tube filled with air. The larynx helps us breathe and create sound when we talk. For this reason, diseases involving the larynx often make it difficult to breathe or talk normally. The inside surface of the larynx is lined by specialized cells called squamous cells. These cells form a barrier called the epithelium. The tissue below the epithelium is called the stroma.

normal squamous mucosa larynx

The larynx is divided into three sections from top to bottom and each section is made up of smaller parts. Most pathology reports will describe the sections or parts of the larynx examined.


The supraglottis is the first section of the larynx. The supraglottic larynx is made up of several smaller parts including:

  • Epiglottis.
  • Aryepiglottic folds.
  • Arytenoids.
  • False vocal cords.
  • Ventricle.

The glottis is the second section and it is in the middle of the larynx. The glottis is made up of several smaller parts including:

  • True vocal cords.
  • Posterior commissure.
  • Anterior commissure.

The subglottis is the third and last section of the larynx. Unlike the other sections of the larynx, the subglottis is not made up of many smaller parts. The subglottic larynx connects with the trachea (windpipe).

What causes squamous carcinoma in situ in the larynx?

The most common cause of squamous carcinoma in situ in the larynx is smoking. Other causes include excessive alcohol consumption, immune suppression, and prior radiation to the neck.

How do pathologists make this diagnosis?

The diagnosis of squamous carcinoma in situ is usually made after a small sample of tissue is removed in a procedure called a biopsy. The biopsy is usually performed because you or your doctor saw an abnormal-looking area of tissue during an examination of your throat. Your pathology report will probably say what part of the larynx was sampled in the biopsy.

The diagnosis of squamous carcinoma in situ can only be made after a tissue sample is examined under the microscope. Compared to normal, healthy squamous cells, the abnormal cells in an area of squamous carcinoma in situ are larger, darker, and disorganized. Pathologists use the word hyperchromatic to describe cells that look darker than normal cells. Large clumps of genetic material called nucleoli may also be seen in the nucleus of the abnormal cells.

larynx squamous carcinoma in situ

The abnormal cells in squamous carcinoma in situ are only seen in the epithelium. This is different from squamous cell carcinoma where the abnormal cells are also seen in the stroma below the epithelium. The movement of abnormal cells from the epithelium into the stroma is called invasion. Your pathologist will carefully examine your tissue sample to make sure there is no evidence of invasion before making the diagnosis of squamous carcinoma in situ.

What to look for in your report after the tumour has been removed

Tumour size

This is the size of the tumour measured in centimetres. The tumour is usually measured in three dimensions but only the largest dimension is described in your report. For example, if the tumour measures 2.0 cm by 1.5 cm by 1.2 cm, your report will describe the tumour as being 2.0 cm.


A margin is any tissue that was cut by the surgeon in order to remove the tumour from your body. Whenever possible, surgeons will try to cut tissue outside of the tumour to reduce the risk that any cancer cells will be left behind after the tumour is removed.


Your pathologist will carefully examine all the margins in your tissue sample to see how close the tumour cells are to the edge of the cut tissue. Margins will only be described in your report after the entire tumour has been removed.

A negative margin means there were no tumour cells at the very edge of the cut tissue. If all the margins are negative, most pathology reports will say how far the closest tumour cells were to a margin. The distance is usually described in millimetres.

A margin is considered positive when there are tumour cells at the very edge of the cut tissue. A positive margin is associated with a higher risk that the tumour will come back (recur) in the same site after treatment.

Lymph nodes

Lymph nodes are small immune organs located throughout the body. Tumour cells can travel from the tumour to a lymph node through lymphatic channels located in and around the tumour. The movement of tumour cells from the tumour to a lymph node is called metastasis.

Lymph node

Lymph nodes are not always removed for squamous carcinoma in situ. When lymph nodes are removed at the same time as the tumour, they are usually from the neck and the procedure is called a neck dissection.

The lymph nodes removed usually come from different areas of the neck and each area is called a level. The levels in the neck include 1, 2, 3, 4, and 5. Your pathology report will often describe how many lymph nodes were seen in each level sent for examination.

Lymph nodes on the same side as the tumour are called ipsilateral while those on the opposite side of the tumour are called contralateral.

Your pathologist will carefully examine each lymph node for tumour cells. Lymph nodes that contain tumour cells are often called positive while those that do not contain any tumour cells are called negative. Most reports include the total number of lymph nodes examined and the number, if any, that contain tumour cells.

Because squamous carcinoma in situ is a non-invasive disease, it is very unlikely that cancer cells will be found in any of the lymph nodes examined.

by Jason Wasserman, MD PhD FRCPC (updated July 28, 2021)
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