A branchial cleft cyst is a birth abnormality that occurs on one or both sides of the neck. This atypical tissue may form fluid-filled sacs or passages that drain fluid on the neck surface.

These cysts occur when structures in the neck and face do not develop typically during gestation, which may lead to anatomical abnormalities.

This article discusses branchial cleft cysts, their types, symptoms, treatment, and more.

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The neck, face, and upper thorax develop from embryonic structures called branchial arches. The word “branchial” derives from the Latin word “branchia,” which means “gills.”

During the fourth week of gestation, there are five branchial or pharyngeal arches split by four depressions known as clefts.

As development ensues, the clefts become buried and typically shrink by 7 weeks of gestation.

However, when these do not shrink or incompletely shrink, the structures may form branchial cleft anomalies. These include cleft lip or palate and branchial cleft cysts.

Branchial cleft anomalies present in three forms:

  • Branchial cleft cyst: This sac has a lining but no external opening that allows communication inside or outside the neck. The sac may fill with fluid and form a cyst.
  • Branchial cleft sinus: The cleft may communicate externally with the skin as a visible opening, which doctors call a punctum, or internally with the pharynx or larynx.
  • Branchial cleft fistula: The cleft connects the pharynx or larynx with the external skin.

A branchial cleft cyst can occur on its own or with a sinus tract or fistula. It presents on the right side in 89% of people with the anomaly.

It is present at birth but may not be noticeable or show symptoms until later. Most become apparent later in life, usually when the fluid develops an infection, causing the formation of a tender neck mass.

Learn more about birth abnormalities.

There are four types of branchial cleft cysts:

First branchial cleft cysts

This type makes up 5–25% of all branchial cleft anomalies. They have two subtypes:

  • Type 1: The opening of this type occurs below or in front of the ear, right above the jawline.
  • Type 2: This type is more common and occurs below the jawline above the hyoid bone. This may also have an internal opening in the ear canal.

Second branchial cleft cysts

This is the most common type, affecting 40–95% of all branchial anomalies. The hole occurs in the front and inner (medial) side of the sternocleidomastoid (SCM) muscle, which develops in the front part of the neck.

If there is an internal opening, it is likely at the back of the throat near the tonsil region.

Third branchial cleft cysts

This cyst comprises 2–8% of all branchial anomalies. If present, the external sinus opening develops over the lower side and front of the SCM muscle. The internal opening connects to the pyriform sinus in the larynx.

Fourth branchial cleft cysts

This type of cyst is extremely rare, comprising 1% of all branchial anomalies. They appear more commonly on the left side of the neck.

This type may loop around the aortic arch in a left-sided anomaly or the subclavian artery in a right-sided anomaly.

The signs and symptoms of a branchial cleft cyst depend on its type.

Symptoms may include a small mass, skin tag, or lump on the side of the neck near the SCM muscle. There may also be a small hole in the skin that drains fluid or mucus.

Cysts can occur in people of any age.

They generally do not cause symptoms except during an acute upper respiratory tract infection. They may become tender, swollen, and enlarged with abscess formation. About 25% of individuals with a branchial cleft cyst report a change in size during an infection.

A person may notice more concerning symptoms if the cyst compresses on the upper airway:

  • dysphagia, or difficulty swallowing
  • dyspnea, or shortness of breath
  • stridor, or wheezing or cracking sounds while breathing

Children with other congenital abnormalities may have a higher risk of having branchial cleft abnormalities. It is common in those with a rare autosomal dominant genetic disease called branchiootorenal syndrome. Autosomal dominant refers to when one parent passes a condition onto their biological child.

Branchial cleft abnormalities can also occur in families, and someone may inherit it as an autosomal dominant trait.

Doctors typically diagnose a branchial cleft cyst with a physical examination.

They diagnose most of them during infancy. They will look for a skin opening that typically pulls back into the skin after a swallowing movement. Lab testing is often unnecessary.

A doctor may carry out the following imaging tests to identify the characteristics of the cyst:

Fine needle aspiration, which involves draining the fluid through a needle, can help doctors identify if the mass is cancerous.

Cysts or sinuses with an infection may require antibiotic treatment and aspiration.

Surgical removal is an elective procedure a person may take due to factors such as:

  • the risk of recurrent infection
  • further enlargement
  • cosmetic appearance
  • the risk of malignancy, though this is very rare

However, immediate surgery may be necessary for large abscesses and compromised airways.

Ethanol ablation is an alternative procedure for individuals who cannot undergo surgery. This is a minimally invasive procedure that destroys cysts using an alcohol solution.

Repeated infections with branchial cleft cysts are common. Reports of infection recurrence after surgery range from 3 to 22%. This is primarily due to the incomplete removal of the cyst.

Other complications involve those commonly occurring in neck operations. These include:

  • hematoma
  • seroma, a buildup of fluid
  • postoperative infection
  • neck scar
  • nerve weakness or paralysis

Squamous cell carcinoma is a rare complication in long-standing cysts.

Another 2021 case study reported the development of a metastatic papillary thyroid carcinoma as a complication of a branchial cleft cyst.

People should speak with a healthcare professional if they notice a small hole, skin tag, or lump in their or their child’s neck or upper shoulder.

This is especially important if fluid drains from the area or if it looks like it may have an infection.

Here are some answers to frequently asked questions about branchial cleft cysts.

Is branchial cleft cyst cancerous?

Branchial cleft cysts are often benign, so cancers arising from them are extremely rare.

Can a branchial cleft cyst go away?

A branchial cleft cyst does not go away on its own and requires surgical removal. However, doctors may treat an infection in a cyst with antibiotics.

A branchial cleft cyst occurs when an embryonic structure called a branchial cleft fails to shrink.

It may show up in different areas in the jaw or neck and present with varying symptoms, depending on the type of branchial cleft cyst. Some may show as a lump, while others may drain fluid in the pharynx or larynx or outside the neck.

Removing the branchial cleft cyst requires surgery, but antibiotics can treat cysts with infections.