Branchial Cleft Cyst

Updated: Jun 02, 2020
Author: Chih-Ho Hong, MD, FRCPC; Chief Editor: William D James, MD 



Branchial cleft cysts are congenital epithelial cysts, which arise on the lateral part of the neck from a failure of obliteration of the second branchial cleft in embryonic development.[1, 2]

Phylogenetically, the branchial apparatus is related to gill slits. In fish and amphibians, these structures are responsible for the development of the gills, hence the name branchial (branchia is Greek for gills).


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.[3, 4, 5, 6]


The branchial cleft cyst is a congenital lesion formed by incomplete involution of branchial cleft structures during embryonic development.



The exact incidence of branchial cleft cysts in the US population is unknown.[1] Branchial cleft cysts are the most common congenital cause of a neck mass. An estimated 2-3% of cases are bilateral. A tendency exists for cases to cluster in families.[7]


No ethnic predilection has been reported for branchial cleft cysts.[1]


No sexual predilection is recognized for branchial cleft cysts.[1]


Branchial cleft cysts are congenital in nature, but they may not present clinically until later in life, usually by early adulthood.


Many branchial cleft cysts are asymptomatic. They may become tender, enlarged, or inflamed, or they may develop abscesses, especially during periods of upper respiratory tract infection, due to the lymphoid tissue located beneath the epithelium. Spontaneous rupture of an abscessed branchial cleft cyst may result in a purulent draining sinus to the skin or the pharynx.

Depending on the size and the anatomical extension of the mass, local symptoms, such as dysphagia, dysphonia, dyspnea, and stridor, may occur.

Following surgical excision of branchial cleft cysts, recurrence is uncommon, with a risk estimated at 3%, unless previous surgery or recurrent infection has occurred, in which case, it may be as high as 20%.

Patient Education

Patients should be reassured that branchial cleft cysts are benign.




A branchial cyst commonly presents as a solitary, painless mass in the neck of a child or a young adult. A history of intermittent swelling and tenderness of the lesion during upper respiratory tract infection may exist. Discharge may be reported if the lesion is associated with a sinus tract.

In some instances, branchial cleft cyst patients may present with locally compressive symptoms. A family history of branchial cleft cysts may be present.

Physical Examination

Primary branchial cleft cyst lesion: Branchial cysts are smooth, nontender, fluctuant masses, which occur along the lower one third of the anteromedial border of the sternocleidomastoid muscle between the muscle and the overlying skin.

Secondary branchial cleft cyst lesion: The lesion may be tender if secondarily inflamed or infected. When associated with a sinus tract, mucoid or purulent discharge onto the skin or into the pharynx may be present.

Rarely, branchial cleft cysts have been reported as fluctuant nodules on the thorax,[8] and even in the posterior mediastinum.[9]



Diagnostic Considerations

Also consider the following:



Laboratory Studies

No specific laboratory investigations need to be obtained in the workup of a branchial cleft cyst.

Imaging Studies

A sinogram may be obtained. If a sinus tract exists, radiopaque dye can be injected to delineate the course and to examine the size of the cyst.

Ultrasonography helps to delineate the cystic nature of these lesions.[11, 12]

A contrast-enhanced CT scan shows a cystic and enhancing mass in the neck. It may aid preoperative planning and identify compromise of local structures. Note the images below.

First branchial cleft cyst, type II. Contrast-enha First branchial cleft cyst, type II. Contrast-enhanced axial computed tomography scan at the level of the hyoid bone reveals an ill-defined, nonenhancing, water attenuation mass (m) posterior to the right submandibular gland (g).
Second branchial cleft cyst. Contrast-enhanced axi Second branchial cleft cyst. Contrast-enhanced axial computed tomography scan at the level of the hyoid bone reveals a large, well-defined, nonenhancing, water attenuation mass (m) on the anterior border of the left sternocleidomastoid muscle(s).

MRI allows for finer resolution during preoperative planning. The wall may be enhancing on gadolinium scans.[11]

Other Tests

No other investigations are needed beyond routine preoperative workup.


Fine-needle aspiration may be helpful to distinguish branchial cleft cysts from malignant neck masses.[13] Fine-needle aspiration and culture may help guide antibiotic therapy for infected cysts.

Histologic Findings

Most branchial cleft cysts are lined with stratified squamous epithelium with keratinous debris within the cyst. In a small number, the cyst is lined with respiratory (ciliated columnar) epithelium. Lymphoid tissue is often present outside the epithelial lining. Germinal center formation may be seen in the lymphoid component, but true lymph node architecture is not seen. In infected or ruptured lesions, inflammatory cells are seen within the cyst cavity or the surrounding stroma.



Medical Care

Antibiotics are required to treat infections or abscesses related to branchial cleft cysts.

Surgical Care

Surgical excision is definitive treatment for branchial cleft cysts.[14] A series of horizontal incisions, known as a stairstep or stepladder incision, is made to fully dissect out the occasionally tortuous path of the branchial cleft cysts. Branchial cleft cyst surgery is best delayed until the patient is at least age 3 months. Definitive branchial cleft cyst surgery should not be attempted during an episode of acute infection or if an abscess is present. Surgical incision and drainage of abscesses is indicated if present, usually along with concurrent antimicrobial therapy.

The traditional surgical approach has the main downfall of relatively significant scarring. Alternatives to the open surgical method have been proposed, including a retroauricular approach, a facelift approach, and endoscopic-assisted removal. All of the newer surgical methods may be limited in the full visualization of the lesion. A case-controlled study suggested that an endoscopic retroauricular approach may provide good surgical clearing with minimal scarring for second branchial cleft cysts.[15, 16]

Sclerotherapy with OK-432 (picibanil) has been reported to be an effective alternative to surgical excision of branchial cleft cysts by some groups,[17] including those using ultrasound guidance.[18]


Referral to an otolaryngologist for surgical excision is indicated.


Untreated branchial cleft cyst lesions are prone to recurrent infection and abscess formation with resultant scar formation and possible compromise to local structures.

Complications of surgical excision of branchial cleft cysts result from damage to nearby vascular or neural structures, which include carotid vessels and the facial, hypoglossal, vagus, and lingual nerves.

There are rare case reports of malignancies having been identified in branchial cleft lesions, including branchiogenic carcinoma and papillary thyroid carcinoma.

Long-Term Monitoring

Postoperatively, patients should be monitored for branchial cleft cyst recurrence. Because some patients have bilateral branchial cleft cyst lesions, the contralateral side should be examined.


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