Cyst, Branchial Cleft

Article Author:
Anouchka Coste
Article Editor:
Carl Shermetaro
10/27/2018 12:31:26 PM
PubMed Link:
Cyst, Branchial Cleft


Branchial cleft cysts are congenital anomalies that usually arise from second cleft/pouch, with remnants of the third and fourth pouch are rare. Children are typically born with these congenital lesions; however, they may not be evident for weeks, months, or possibly years. The lesions present as fistulae, cyst, sinus tracts, or cartilaginous remnants due to incomplete obliteration during embryogenesis. Cysts have a mucosal or epithelial lining without external openings. Sinus tracts may communicate either externally with skin or external with the skin or internally with the pharynx, compared to fistulae that connect to both.


The cause of branchial cleft cyst is incomplete involution of branchial cleft structures. Around the fourth week of gestation, neural crest cells migrate into the future head and neck region where 6 pairs of branchial (pharyngeal) arches begin to develop. The mesoderm is covered externally by ectoderm and internally lined by endoderm. Typically there are 5 branchial arches. The arches are separated by depressions known as clefts (i.e., ectoderm surface) and pouches (i.e., endoderm surface), with typically 4 pharyngeal clefts. The second arch develops caudally and then covers the third and fourth arches. These buried clefts become ectoderm-lined cavities that will usually involute completely by 7 weeks of gestation. However,  if the clefts do not involute, they will form pathological remnants of the epithelium-lined cyst, with or without a sinus tract over the skin.


The actual incidence of branchial cleft cyst in the United States is unknown, despite being the most common congenital cause of neck masses. There is no ethnic or gender predilection. Most branchial cleft anomalies arise from the second pouch, while the third and fourth pouches are rare. These cysts typically occur in the first decade of life when sinuses are present, but if no sinuses are present, then the patient will usually have delayed presentation into adulthood. Ten percent of all lesions are bilateral.


Branchial cleft cysts are embryologic anomalies in origin and are defined by the internal opening of the branchial sinuses arising from incomplete obliteration in embryogenesis. They may present as fistulae, cysts, sinus tracts, or cartilaginous remnants and clinically encountered on the anterior neck and upper chest. Lesions presenting below the clavicles are more likely epidermoid or dermoid cysts rather than branchial remnants. Branchio-oto-renal (BOR) and branchio-oculo-facial (BOF) syndromes should be suspected when a patient presents with preauricular pits with branchial anomalies. These syndromes are autosomal dominant conditions typically associated with hearing loss, ear malformations, and renal anomalies in the BOR syndrome, while BOF includes eye anomalies, such as microphthalmia and obstructed lacrimal ducts, and facial anomalies, such as cleft or pseudocleft lip/palate.


Branchial cleft cysts are lined with stratified squamous epithelium and contain keratinous debris inside the cyst. In some cases, the cyst wall is lined by ciliated columnar epithelium. Lymphoid tissue is typically present surrounding the epithelial lining. If the cyst is infected or ruptured, inflammatory cells can be identified in the cavity or stroma.

History and Physical

Branchial cleft cysts are often asymptomatic, but can often become tender, enlarged, or inflamed with possible abscess formation during episodes of upper respiratory tract infections. The patient can present with purulent drainage of the sinus to skin or pharynx from spontaneous rupture of branchial cleft cyst abscess. The most concerning symptoms include dysphagia, dyspnea, and stridor due to cyst compression of the upper airway.

Physical examination will differ depending on the location of the branchial cleft cyst.

  • A primary branchial cleft cyst is typically smooth, non-tender, fluctuant mass found between the external auditory canal and submandibular area. It is usually with the parotid gland and facial nerve. Two types of lesions exist. Type 1 is rare and characterized as duplication of the membranous external auditory canal. Type 2 lesions contain both ectoderm and mesoderm elements including cartilage. The patient usually presents with soft tissue mass or draining sinus located on the angle of the mandible or otorrhea, making an otologic exam critical in these cases.
  • A secondary brachial cleft cyst is located between the lower anterior border of the sternocleidomastoid and the tonsillar fossa of the pharynx. It can be in proximity to the glossopharyngeal and hypoglossal nerve as well as carotid vessels. Compared to the primary branchial cleft cysts,  secondary cysts are tender if secondarily inflamed or infected. If it is associated with a sinus tract, mucoid or purulent discharge may be present on the skin or into the pharynx.

Epithelium lines the branchial anomalies. Cystic lesions are more common than fistulae, but they usually present later, usually in the second decade of life. Cysts most often present as non-tender soft tissue masses beneath the SCM muscle. However, they may present with acute infection. Change in size during upper respiratory infections is noted in up to 25%. The anomalies have been classified into 4 types. Type-1 anomalies are superficial but located deep to the platysma and cervical fascia, along with the anterior border of the SCM muscle. Type-2 anomalies are the most frequent. They run deep to the SCM muscle and anterior or posterior to the carotid artery. Type-3 lesions occur between the carotid bifurcation and rest adjacent to the pharynx. Type-4 lesions are medial to the carotid sheath and close to the pharynx at the level of the tonsillar fossa.

Third and fourth branchial cleft cysts are rare. They are normally on the left side of the neck or the suprasternal notch/clavicular area. Typically they present as a firm mass or infected cyst draining to the piriformis sinus tract. The fistula is usually seen infected, or patients have repeated surgery for their branchial cleft anomalies.


There is no specific laboratory test needed for evaluation. 

Imaging Studies

  • If a sinus tract present, a sinogram can be obtained by injecting radiopaque dye to delineate the course and determine the size of the cyst.
  • Ultrasonography can be obtained to determine the cystic characteristics of the cyst.
  • Contrast-enhanced CT will depict a cystic and enhanced mass in the neck. 
  • MRI can be used for a finer resolution.

Fine-needle aspiration is helpful to distinguish a branchial cleft cyst from malignant neoplasm.

Treatment / Management

The treatment of a branchial cleft cyst is typically elective excision due to the risk of infection or present infection, further enlargement, or malignancy. There is typically no urgency; clinicians can defer excision beyond 3 to 6 months of age or allow treatment of an acute infection. Systemic antibiotics and aspiration are generally preferable to incision and drainage which might produce more distortion of the surgical planes. However, when the diagnosis is unclear, the latter allows biopsy of the cyst wall, and this can help to differentiate between an infected branchial cleft cyst and simple bacterial lymphadenitis.

In general, a transverse incision is usually made directly over the cyst for cosmesis, however, if fistula or sinus is present then identifying the tract by gentle insertion of a probe or catheter is important. Methylene blue can be used by dipping a lacrimal probe in the solution and inserting into the tract for staining, in the event that the track should break during excision. Dissection should be performed carefully over the surface of the lesion as the tract can be thin-walled. If the tract is long, then exposure should be obtained by using a "stepladder" incision along the skin crease cephalad to the primary incision. It is important to ensure that vital structures are not damaged as well. In primary branchial cleft cyst, initial exposure of the main trunk of the facial nerve and branches should be performed with superficial parotidectomy to reduce the risk of facial nerve injury.

Third and fourth branchial cleft cysts are treated with a standard collar incision to identify the recurrent laryngeal nerve along with a partial or total ipsilateral thyroid lobectomy with excision of the tract to the piriform sinus. Removal of the entire tract may require partial resection of the thyroid cartilage with cauterization of the internal opening as well. Before surgery, direct laryngoscopy or rigid pharyngoscopy is usually performed for accurate diagnosis, and endoscopic cannulation of the opening into the piriform sinus is done to improve dissection during excision.

Differential Diagnosis

Differentials include:

  • Lymphadenopathy
  • Hemangioma
  • Carotid body tumor
  • Cystic hygroma
  • Ectopic thyroid/salivary tissue
  • Vascular neoplasm/malformation


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


Once branchial cleft cysts are excised, recurrence is relatively uncommon. There is an estimated risk of 3%. However, if previous surgery or recurrent infection has occurred, recurrence can be as high as 20%.


Otolaryngologist or an experienced pediatric surgeon should be consulted in these cases depending on the age of the patient.