Branchial Cleft Cyst


What is a branchial cleft cyst?

Branchial cleft cysts are small fluid-filled sacs that may look like lumps under your skin on the side of your neck. Healthcare providers may refer to branchial cleft cysts as pharyngeal cleft cysts or as a type of neck mass.

These cysts are congenital, meaning they’re present at birth. Branchial cleft cysts appear at any age, but children are more likely than adults to be diagnosed with them. People can develop noticeable branchial cleft cysts later in life. This usually happens when the cysts are infected.

Branchial cleft cysts are benign, but healthcare providers may recommend surgery to remove the cyst to prevent or treat infections or recurrent (returning) swelling.

How rare is a branchial cleft cyst?

Healthcare providers aren’t sure if branchial cleft cysts are rare or common. That’s because not all branchial cleft cysts cause problems. That said, branchial cleft cysts are one of the most common forms of neck masses or lumps, especially in children.

Symptoms and Causes

What causes a branchial cleft cyst?

Branchial cleft cysts happen during gestation, as your body is building the foundation for your head and neck structure, including your larynx (voice box), your mandible (upper jaw) and your hyoid bone, which supports your tongue.

Here’s how that process works:

  • Neural crest cells, which develop tissues, gather in the area of your head and neck to create what’s called your branchial apparatus.
  • Your branchial apparatus becomes cartilage, bone, blood vessels and the muscles in your head and neck.
  • Your branchial apparatus has ridges of tissue (arches) and in-foldings of tissue (clefts) that are responsible for developing certain parts of your head and neck. All told, there are six arches and five clefts.
  • Branchial cleft cysts happen when branchial arches don’t fuse, or grow together. Think of these arches as hamburger patties on a plate. Your body needs to compress these patties to make one larger patty. When spaces are left between the patties, branchial anomalies, including branchial cleft cysts, fistula and sinuses, develop.

What are the branchial cleft cyst types?

Healthcare providers categorize branchial cleft cysts by the arch and cleft. Here is information about those types:

Branchial cleft cyst typeIncidenceLocation and impact
First branchial cleft cystFirst branchial cleft cysts make up approximately 5% to 25% of all branchial cleft anomalies. There are two first cleft cyst sub-types.First branchial cleft cysts are located between your ear and the submandibular area. That’s the area between your lower jaw and your hyoid bone. Your hyoid bone supports your tongue. First branchial cleft cysts can affect your middle or external ear.
Second branchial cleft cystThis is the most common branchial cleft cyst, representing approximately 40% to 95% of branchial anomalies.These cysts usually appear under the skin of your neck muscle. People often notice second branchial cleft cysts when they develop upper respiratory infections. You can have second branchial cleft cysts on both sides of your neck.
Third/fourth branchial cleft cystsThese cysts are rare.They’re usually found under your skin on the left side of your neck or at the bottom of your neck near your collarbone. These cysts can affect your thyroid gland.

What are branchial cleft cyst symptoms?

Many branchial cleft cysts don’t have symptoms. That’s why healthcare providers can’t say if these cysts are common. But when branchial cysts do cause problems, some symptoms you might notice include:

  • A painless lump or swollen area under the skin of your neck that appears when you have upper respiratory infections. The lump may be larger at the start of your infection and then shrink as you get better.
  • A painful lump or swelling under the skin on your neck. This can happen if your branchial cleft cyst becomes infected.
  • Some cleft cysts might ooze fluid through the punctum, which is a tiny point at the top of your cyst.
  • You have difficulty swallowing food. Sometimes, branchial cleft cysts grow large enough to affect your ability to swallow.
  • You have a tight feeling in your chest when you take a deep breath.

Diagnosis and Tests

How do healthcare providers diagnose branchial cleft cysts?

Healthcare providers will examine your neck and ask about your symptoms. They may do the following radiology studies:

  • Computed tomography (CT). CT scans use a series of X-rays and a computer to create three-dimensional (3D) images of the soft tissues and bones in your head and neck.
  • Magnetic resonance imaging (MRI). This is a painless test that uses a large magnet, radio waves and a computer to produce very clear images of organs and structures within your head and neck.
  • Chest X-ray. A chest X-ray uses a focused beam of radiation to look at your heart, lungs and bones.
  • Ultrasound. Ultrasounds use high-frequency soundwaves to create real-time pictures and videos of your internal organs or other tissues.
  • Hearing examination. Healthcare providers may recommend this if you have a first branchial cleft cyst.

Management and Treatment

Do branchial cleft cysts need to be removed?

Yes. Even if your cleft cyst isn’t causing problems, your healthcare provider will likely recommend surgery to remove your cyst and eliminate the chance of your cyst becoming infected.

What is the treatment for each branchial cleft cyst type?

Each branchial cleft cyst type might require different treatment. Some potential treatments your healthcare provider may recommend include:

  • Antibiotics to treat infected cysts.
  • Surgery to remove the cysts.
  • Partial thyroidectomies. This surgery is recommended if you have third/fourth branchial cleft cysts that affect your thyroid.


Can I prevent branchial cleft cysts?

No, these cysts are congenital conditions, meaning you were born with them.

Outlook / Prognosis

What can I expect if I have a branchial cleft cyst?

Surgery to remove your cyst usually solves the problem. Very few branchial cysts recur, or come back, after being surgically removed.

Living With

When should I see my healthcare provider?

If you’ve had surgery to remove a branchial cleft cyst, your healthcare provider will give you specific instructions on caring for your surgery site. You should contact your healthcare provider if:

  • You have a fever higher than 101 Fahrenheit (38.3 Celsius).
  • You have pain that isn’t helped by the medications prescribed for you.
  • You have more drainage or swelling than you expected.

What questions should I ask my healthcare provider?

Children and adults can have branchial cleft cysts that cause painful symptoms. If you or your child have these cysts, some questions you may want to ask your healthcare provider include:

  • Why do I/does my child have cysts?
  • Is this cyst cancerous?
  • Can this cyst become cancerous?
  • Will my cyst/my child’s cyst go away on its own?
  • What’s the treatment?
  • What are typical treatment side effects?

A note from Cleveland Clinic

It may be unnerving to find an unusual lump on your or your child’s neck, even if the lump doesn’t hurt. Many times, mysterious lumps turn out to be cysts, such as branchial cleft cysts that are benign and that your healthcare provider can remove surgically. Talk to your healthcare provider any time you notice a lump on your neck or your child’s neck. They’ll diagnose the problem and recommend treatment.

Last reviewed by a Cleveland Clinic medical professional on 03/17/2022.


  • Allen Samantha B, Jamal Zohaib, Goldman Julie. Branchial Cleft Cysts. ( StatPearls. Accessed 3/17/2022.
  • American Family Physician. Evaluation of Neck Masses in Adults. ( Accessed 3/17/2022.
  • Bagchi Antara, Hira Priya, Dey Amit K. Branchial Cleft Cysts: A Pictorial Review. ( Pol J. Radiol. Accessed 3/17/2022.
  • Coste AH, Lofgren DH, Shermetaro C. Branchial Cleft Cyst. ( StatPearls. Accessed 3/17/2022.
  • Mehmi N, Kumar R, Sagar P. Importance and Impact of Appropriate Radiology in the Management of Branchial Cleft Anomalies. ( Indian J Otolaryngol Head Neck Surg. Accessed 3/17/2022.
  • Prasad SC, Azeez A, Thada ND. Branchial Anomalies: Diagnosis and Management. ( Int J Otolaryngol. Accessed 3/17/2022.

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