Branchial Cleft Cysts

Branchial Cleft Cysts

Branchial Cleft Cysts

Branchial cleft cysts (also called branchial cleft remnants or branchial cleft anomalies) are a congenital condition (condition present at birth) in which tissue develops incorrectly on one or both sides of the neck. Branchial cleft cysts sometimes have openings on the inside or outside of the skin called sinus tracts. Fluid may drain from the openings.

  • Sinus tracts occur when there is one opening in the skin where fluid may drain out of a small hole in the neck.
  • Branchial fistulas occur when one opening forms specifically between the skin and throat lining (pharynx), draining mucus out of the neck.
  • Branchial cleft cysts occur when there is no external opening and liquid cannot drain out of the neck. Then, a collection of fluid forms. A brachial cyst can occur on its own or with a branchial cleft sinus tract or fistula.


Branchial cleft cysts and sinus are congenital conditions

(conditions present at birth) caused by unexpected changes during pregnancy. Often, these changes occur around the 5th week of pregnancy, when gill-like structures around the neck do not reabsorb back into the skin. At the same time, pharyngeal arches (bands of tissue that develop into the head and neck) start to form. Later, these arches become bone, cartilage, muscles and blood vessels. When these arches form incorrectly, they create empty spaces that fill with fluid and become cysts. Most of the time these conditions are unilateral (occur on one side of the neck). When branchial cleft cysts are bilateral (on both sides), your child is more likely to have other congenital abnormalities (conditions present at birth).

Types of branchial cleft abnormalities

There are several types of branchial cleft abnormalities.

  • First branchial cleft anomalies. These are cysts around the earlobe or under the jaw, with an opening below the jaw and above the larynx, or voice box. This type is rare.
  • Second branchial cleft sinuses. These 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 your child’s neck. These cysts generally appear after age 10. This is the most common type of branchial cleft abnormality.
  • Third branchial cleft sinuses. These are near the thyroid gland in the front part of the muscle that attaches to your child’s collarbone. This type is very rare.
  • Fourth branchial cleft sinuses. These are below the neck. This type is also quite rare.

In most cases, a branchial cleft cyst isn’t dangerous. However, the cyst can drain and cause skin irritation. Cysts can also become infected, causing difficulty with swallowing and breathing. Cancerous tumors may develop at the site of a branchial cleft in adults, but this is very rare.

Symptoms of Branchial Cleft Cysts and Sinus Tracts

Some branchial cleft cysts go unnoticed until your child develops an upper respiratory infection, like the common cold. Unless the cyst is infected, it is usually not painful.

Possible symptoms include:

  • Lump or skin tag on neck or upper shoulder
  • Bumps that become more painful with swallowing/ grow bigger over time
  • Swelling or tenderness on neck, sometimes occurring during or after an upper respiratory infection
  • Fluid exiting neck from a small dimple or opening in skin

If the cyst is infected, possible symptoms include:

  • Painful bump in the neck
  • Trouble with swallowing
  • Skin itching and irritation

If your child has any of these symptoms, tell the pedi atrician. They will likely refer you to a pediatric surgeon.



Most of the time, a doctor will diagnose this condition during a physical exam. Diagnostic imaging tests to determine the exact location may include an MRI scan, a CT scan, or an ultrasound.

Additional diagnostic testing may include a microscopic examination of the fluid from a fine needle aspiration. In this procedure, your child’s doctor inserts a small needle into the cyst to remove fluid for analysis. They may also examine tissue from a biopsy.


Infected branchial cleft cysts or sinuses require antibiotic treatment. If there are persistent problems with drainage or infection, these cysts should be surgically removed. Most branchial cleft remnants require no treatment. If surgery is required, results are usually good.


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