Branchial Cleft Cyst – Complications, Symptoms, and Prevention.

What is a branchial cleft cyst?

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

This birth defect occurs during embryonic development when tissues in the neck and collarbone, or branchial cleft, don’t develop normally. It may appear as an opening on one or both sides of your child’s neck. Fluid draining from these openings may form in a pocket, or a cyst. This can become infected or seep out of an opening in your child’s skin.

Types of Branchial Cleft Cyst

There are four main types of Branchial cleft abnormalities

  • First branchial cleft anomalies, in which cysts develop around the earlobe or under the jaw
  • Second branchial cleft sinuses, which open on the lower part of the neck
  • Third branchial cleft sinuses, which develop close to the thyroid gland in the front part of the muscle which attaches to the collarbone
  • Fourth branchial cleft sinuses, which affect the area below the neck.

The most common type of Branchial cleft abnormality is ‘Second branchial cleft sinuses,’ or the failure of fusion of the second and third branchial arches.


At the fourth week of embryonic life, the development of 4 branchial (or pharyngeal) clefts results in 5 ridges known as the branchial (or pharyngeal) arches, which contribute to the formation of various structures of the head, the neck, and the thorax. The second arch grows caudally and, ultimately, covers the third and fourth arches. The buried clefts become ectoderm-lined cavities, which normally involute around week 7 of development. If a portion of the cleft fails to involute completely, the entrapped remnant forms an epithelium-lined cyst with or without a sinus tract to the overlying skin.

What are the causes and risk factors of a branchial cleft cyst?

This is a congenital birth defect that occurs early in embryonic development. Major neck structures form during the fifth week of fetal development. During this time, five bands of tissue called pharyngeal arches form. These important structures contain tissues that’ll later become:

  • Cartilage
  • Bone
  • Blood vessels
  • Muscles

Several defects in the neck can occur when these arches fail to develop properly.

In branchial cleft cysts, the tissues that form the throat and neck don’t develop normally, creating open spaces called cleft sinuses on one or both sides of your child’s neck. A cyst may develop from fluids that are drained by these sinuses. In some cases, the cyst or sinus may become infected.

Symptoms of Branchial Cleft Cyst

Branchial cleft cyst mostly does not cause any pain, except in cases when it gets infected. Some of the symptoms of a branchial cleft cyst include:

  • Pain in the affected area.
  • Feeling of pressure in the affected area.
  • Draining of fluid from the neck of the child.
  • Formation of a small lump or mass on the side of the neck close to the front edge of the sternocleidomastoid muscle.
  • Formation of a lump, dimple or skin tag on the child’s upper shoulder, or slightly underneath their collar bone.
  • Swelling or tenderness in the child’s neck, generally occurring with an upper respiratory infection.

Branchial cleft cysts generally develop in late childhood or early adulthood as a solitary, painless mass which becomes infected, though it is not noticed earlier.

Complications of Branchial Cleft Cysts

  • If branchial cleft cysts are left untreated, they’re prone to abscess formation and recurrent infection with a potential compromise to local structures and resultant scar formation.
  • Although rare, there have been reports of malignancies in branchial cleft cysts, including papillary thyroid carcinoma and branchiogenic carcinoma.
  • The outcome of surgery is usually good. But, cysts can recur, particularly if the surgery occurred during an active infection. Experiencing a little pain following surgery is normal, but if it gets worse and doesn’t go away, it could indicate bleeding or infection.
  • The surgeon makes every effort to completely remove the cyst. Sometimes, it can have tracts that the surgeon doesn’t detect during surgery. Most patients have the cyst removed successfully with just one surgery and no additional problems. You may need another surgery if it does recur to completely remove it.

Diagnosis of Branchial Cleft Cysts

  • A correct diagnosis will lead to proper management. Complete history and physical exam is usually all that is necessary for diagnosis. The classic fistula/sinus opening in the usual location, with mucous drainage, is specific for a branchial anomaly.
  • Ultrasound confirms the diagnosis and can usually trace if there is an internal opening (fistula).
  • CT or MRI may be needed if there is more information needed or if the diagnosis is not definite.
  • Depending on how sure the doctors are of the diagnosis, other studies might be ordered.

Conditions that mimic this condition

  • Dermoid cysts: Growth from skin elements
  • Thyroid nodules: Growth in the thyroid gland
  • Lymph nodes: Small nodules in the neck that enlarge in response to infection.
  • Skin infections such as boils or abscesses

Treatment and Medication


No medications are usually needed. If the cyst, sinus or fistula is infected, medicines (antibiotics) are given to control infection.


Removal of the cyst, fistula or sinus is the treatment of choice.

  • If the structure is infected, the infection must be treated first with antibiotics. Sometimes, control of the infection needs draining the pus from underneath the skin.
  • Abnormalities on the face may connect to the ear canal. Therefore, children with these lesions on the face are usually referred to pediatric ear/nose and throat surgeons.
  • Abnormalities of the neck are studied to see the entire structure along with internal openings. The sinus/ fistula or cyst is completely removed. Sometimes, a second small incision made higher in the neck is needed for complete removal. Usually the wound is closed with dissolving sutures, and there are no sutures to remove.

Preoperative preparation

Patients are usually asked to shower or bathe on the night before surgery. Patients are asked to stop eating or drinking for a few hours before surgery.

  • Informed consent: A consent form is a legal document that states the tests, treatments or procedures that your child may need and the doctor or practitioner that will perform them. You give your permission when you sign the consent form.
  • Emotional support: Stay with your child for comfort and support as often as possible while he or she is in the hospital. Bring items from home that will comfort your child, such as a favorite blanket or toy.

Postoperative care

Depending on the extent of the surgery, the patient goes home on the same day of the operation or stays in the hospital overnight.


  • Benefits of surgery: Confirm the diagnosis, prevent infection, and decrease the risk that the lesion could become malignant.
  • Risks of surgery: Bleeding, damage to nerves or neck structures, post-operative scar, risk of anesthesia, rare swelling around the airway that may interfere with breathing. The patient may be observed in hospital overnight if this is a concern.

Home Care

  • Diet: Your child may eat a normal diet after surgery.
  • Activity:  Your child should avoid strenuous activity first 1-2 days.
  • Wound care:  Surgical incisions should be kept clean and dry for a few days after surgery. Most of the time, stitches used in children are absorbable and do not require removal. Your surgeon will give you specific guidance regarding wound care, including when your child can shower or bathe.
  • Medicines:  Medicines for pain such as acetaminophen (Tylenol) or ibuprofen (Motrin or Advil) or something stronger like a narcotic may be needed to help with pain for a few days after surgery. Stool softeners and laxatives are needed to help regular stooling after surgery, especially if narcotics are still needed for pain.
  • What to call the doctor for:  Neck swelling or shortness of breath are serious signs that there is bleeding or swelling that is affecting breathing. The patient should go to the emergency room. Fever, redness of the incision or fluid draining from the wound can be signs of post-operative infection.
  • Follow-up care:  Follow-up visit with the surgeon a few weeks after operation.


Patients and families should be educated that branchial cleft cysts are typically benign, and with treatment, patients generally recover without complications or recurrence.

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