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.

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
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.
There are four types of branchial cleft cysts:
First branchial cleft cysts
This type makes up
- 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
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
Fourth branchial cleft cysts
This type of cyst is extremely rare, comprising
This type
The signs and symptoms of a branchial cleft cyst depend on its type.
Symptoms may
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:
Children with other congenital abnormalities may have a higher risk of having branchial cleft abnormalities. It is
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
A doctor may carry out the following imaging tests to identify the characteristics of the cyst:
- a dye injection test
- a cervical ultrasound
- a contrast-enhanced CT scan
- an MRI
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
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
Other complications involve those commonly occurring in neck operations. These include:
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
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.