Branchial Cleft Cyst

What is a branchial cleft remnant?

A branchial cleft remnant is a developmental abnormality that occurs in your child's neck, usually on the side of the neck above the collar bone. It occurs during early embryonic development when the tissues that form the neck and throat do not properly grow together. They may be cysts, sinuses or fistulas. Cysts are fluid filled lumps underneath the skin. Sinuses are small passageways that may have an opening into the skin or the back of the mouth.  A fistula means there is communication between the small skin opening and one in the back of the mouth.

There are three kinds of branchial cleft cysts and sinuses. The most common type (about 90%) is the second branchial cleft cyst which is found in the lower part of the neck between the large neck muscle, the sternocleidosmastoid and the trachea (windpipe). They are related to the development of the tonsils. The much more rare types, the first and third branchial cleft cysts or sinuses may have openings just below the jaw and on the chest wall just below the collar bone, respectively. While the external opening is small, the tract often will course between blood vessels and nerves in the neck towards the back of the mouth or the ear.


Your child’s physician can often diagnose them after a thorough physical exam. A history of infection or drainage (often of saliva) from small openings on the neck and acute or chronic swelling in the neck are also reliable signs. Your doctor may also order an ultrasound of the neck, and in select cases, other image studies or endoscopy to help confirm the diagnosis.

How are branchial cleft abnormalities treated?

Infection is the main indication for removal. A branchial cleft cyst may become infected when your child has a sore throat, cold or ear infection. The cyst is located in the neck near a vast supply of lymph nodes that monitor all infections in the head and neck area. Once the branchial cleft cyst becomes infected, it may begin to drain thick yellow fluid. The skin over the cyst may also become red and swollen. Infected cysts are treated with oral antibiotics and warm compresses. Occasionally the infected cyst may need to be opened and drained. If there are persistent problems with drainage or infection, these cysts should be surgically removed. Excision of the cyst or tract would not be performed in the period of acute infection due to inflammation of surrounding tissue. If your child has chronic drainage without signs of infection, surgical excision is also recommended due to the future risk of infection. During the operation a complete removal of branchial cleft remnants is performed.

What will happen in the hospital?

The operation is usually done as a day surgery procedure under general anesthesia. The surgery is done through an elliptical incision in the skin around the opening of the branchial cleft cyst. The cyst or sinus is then traced superiorly, carefully avoiding blood vessels and nerves. Sometimes a small second more superior incision (also called a “stepladder” incision) is necessary for full excision of the cyst depending on how far it extends. Often it cannot be determined before surgery if this will be necessary.

Bleeding and infection are minor surgical risks. Recurrence of the cyst is also rare, but can occur. The surgeon will talk to you when your child's surgery is over. Your child will go to the recovery room (often called a post-anesthesia care unit/PACU) to allow the anesthesia to wear off. After the surgery, your child may have the following symptoms:
  • Pain, soreness and swelling around the surgical incision site 
  • Nausea and vomiting (from general anesthesia, pain medicine and surgery) 
  • Throat soreness (caused by a tube placed in the windpipe to assist breathing during surgery) 
  • Restlessness or sleeplessness, and may have some dizziness especially when getting out of bed for the first time.
After your child wakes up they will be given clear liquids, such as water, ginger ale, apple juice and popsicles.

When will my child be discharged?

Usually, once your child is awake, able to tolerate some food and their pain is well controlled they will likely be discharged from the PACU. The operation is usually done as a day surgery but an overnight stay may be needed for operations done deep in the neck.

What will be my child's recovery?

Your child should not do any strenuous exercise or activity for five to seven days after the surgery. The Band-aid or steri-strips should remain in place for at least ten days after the surgery. You will be instructed to follow up in one to two weeks in the pediatric surgery clinic. Usually over the counter Tylenol is more than sufficient for adequate pain control.

What should I be looking out for after the operation?

In the first several days and week after surgery it is important to monitor for signs or symptoms or infection such as redness, swelling around the surgical site or fever. Recurrence of the cyst or sinus is possible, months to years later and is more common when the operation is done at the time of an active infection when complete cyst excision may be more challenging.