Branchial Cleft Cyst

Written by Ann Pietrangelo | Published on September 13, 2012
Medically Reviewed by George Krucik, MD

What is a Branchial Cleft Cyst?

A branchial cleft cyst is a type of birth defect in which a lump develops in one or both sides of a child’s neck or below the collarbone. This type of birth defect is also called branchial cleft remnant.

This defect occurs during fetal development when tissues in the neck and collarbone, or branchial cleft, do not develop normally. It may appear as an opening on one or both sides of the neck. Fluid draining from these openings may form a pocket, or a cyst, which can become infected or seep out of an opening on the skin.

Diagnosis is usually made upon physical examination. If there are signs of infection, your doctor will likely prescribe antibiotics. Surgical removal may be recommended to prevent repeat infections.

Cause of Branchial Cleft Cysts

This is a congenital birth defect that occurs early in embryonic development. Major neck structure is formed during the fifth week of fetal development. During this time, five bands of tissue (pharyngeal arches) are formed. These important structures contain tissues that will later become cartilage, bone, blood vessels, and muscles. When these arches fail to develop properly, it can result in several defects in the neck.

In branchial cleft cysts, the tissues that form the throat and neck do not develop normally, forming open spaces (cleft sinuses) on one or both sides of the neck. A cyst may form from fluids that are drained by these sinuses. In some cases, the cyst or sinus may become infected.

Types of Branchial Cleft Abnormalities

There are four types of branchial cleft abnormalities:


First branchial cleft anomalies are cysts that are found around the earlobe or under the jaw, with an opening below the jaw and above the larynx (voice box). This type of branchial cleft abnormality is rare.


Second branchial cleft sinuses are sinus tracts that open on the lower part of the neck. They may go as far as the tonsil area. You may be able to see skin tags or feel the tract opening as a band in the neck. Cysts generally appear after age 10. This is the most common type of branchial cleft abnormality.


Third branchial cleft sinuses are near the thyroid gland in the front part of the muscle that attaches to the child’s collarbone. This type is very rare.


Fourth branchial cleft sinuses are found below the neck. This type is also quite rare.

In most cases, a branchial cleft cyst is not dangerous. However, the cyst can drain and cause skin irritation. Cysts can also become infected, causing difficulty with swallowing and breathing. According to Boston Children’s Hospital, cancerous tumors may develop at the site of a branchial cleft in adults, but this is very rare (BCH).

Signs and Symptoms of a Branchial Cleft Cyst

A branchial cleft cyst usually doesn’t cause pain unless there is infection. Signs of a branchial cleft cyst include:

  • dimple, lump, or skin tag on the neck, upper shoulder, or slightly below the collarbone
  • fluid draining from the neck
  • swelling or tenderness in the neck, usually in conjunction with an upper respiratory infection

If your child has signs of branchial cleft cyst, make an appointment with your pediatrician.

Diagnosing a Branchial Cleft Cyst

Most of the time, this condition is diagnosed during a physical exam. Diagnostic imaging tests to determine the exact location may include magnetic resonance imaging (MRI), computed tomography (CT) scan, or ultrasound.

Additional diagnostic testing may include microscopic examination of the fluid (fine needle aspiration) or tissue (biopsy).

Treatment for Branchial Cleft Cysts

If there are signs of infection, your doctor will likely prescribe antibiotics. It may be necessary to drain fluid from the cyst to ease swelling. To prevent future infections, surgery to remove the cyst is usually recommended.

The surgery is usually done on an outpatient basis and is performed under general anesthesia, meaning that your child will be asleep and pain-free during the procedure. Your child will be unable to take a bath or engage in active play for a few days following surgery. Bandages can be removed within five to seven days after surgery.

Long-Term Outlook

Surgery usually results in a good outcome. However, the cysts can recur, especially if surgery was performed during an active infection (BCH).

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