Definition: Branchial cleft cysts are congenital anomalies arising from the 1st to 4th pharyngeal clefts. The most common type of branchial cleft cyst arises from the 2nd cleft, with anomalies derived from the 1st, 3rd and 4th clefts being rarer. 


Branchial cleft anomalies form due to the incomplete involution of branchial cleft structures. Around the 4th week of gestation, neural crest cells migrate into the future head and neck region where the 6 pairs of branchial (pharyngeal) arches begin to develop. The mesoderm is covered externally by ectoderm and internally lined by endoderm. Normally there are 5 branchial arches. The arches are separated by depressions known as clefts on the ectodermal surface and corresponding pouches on the endodermal surface, giving 4 pharyngeal clefts. The 2nd arch develops caudally and then covers the 3rd and 4th arches. These buried clefts become ectoderm-lined cavities that normally involute completely by 7 weeks of gestation. If the clefts do not involute, or incompletely involute, these pathological remnants will form cysts, sinuses, or fistulae in predictable locations according to their branchial cleft of origin.

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1st Branchial cleft cyst

1st cleft cysts make up approximately 5-25% of all branchial cleft anomalies. It is subclassified via the Work classification system:

Work type I contain ectoderm only and on physical exam show preauricular masses or sinuses that track anterior and medial to the external auditory canal. These typically present lateral to the facial nerve and end within the external auditory canal or connect to the umbo of the middle ear essentially as a duplication of the external auditory canal. 

Work type II cysts are more common, and contain both ectoderm and mesoderm. These classically present at the angle of the mandible or within the submandibular region. They can be course either lateral or medial to the facial nerve and pass superficial, deep or between branches of the facial nerve.

2nd Branchial cleft cyst

This is the most common branchial cleft cyst, representing approximately 40-95% of branchial anomalies.  The external punctum is found anterior and medial to the sternocleidomastoid (SCM) on the neck skin. 

Bilateral 2nd branchial cleft cysts can be associated with branchio-oto-renal syndrome. 

The course of a 2nd branchial cleft sinus is as follows:

  1. The external opening is located on anterior and medial to the sternocleidomastoid (SCM) on the neck skin. 
  2. The fistula travels deep to platysma then passes in between the internal and external carotids, coursing superficial to both glossopharyngeal and hypoglossal nerves before connecting to the tonsillar fossa.

There is a slight left-sided predominance.

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3rd Branchial cleft cyst

3rd branchial cleft cysts are estimated to represent 2-8% of all branchial cleft anomalies. When present, the external skin opening is seen over the middle to lower third of the anterior SCM. 

The course of the 3rd branchial cleft sinus is as follows: 

1) The external skin opening over the middle to lower third of the anterior SCM.

2) The tract courses deep to platysma and posterior to the internal carotid artery.

3) It then passes between the glossopharyngeal and hypoglossal nerves, and may be intimately associated with superior laryngeal nerve. 

4) Finally, it connects to the pyriform sinus in the larynx.

4th Branchial cleft cyst

4th cleft cysts are extremely rare, representing approximately 1% of all branchial cleft anomalies. 

They are reported more commonly on the left, with the skin opening near the medial lower border of the SCM. 

The course of the 4th branchial cleft remnant is as follows: 

1) It classically passes deep to the common carotid and can loop around either the aortic arch (in a left-sided anomaly) or the subclavian (in a right-sided anomaly).

2)Then they run superficial to the recurrent laryngeal nerve and hypoglossal nerve terminating in the apex of the pyriform sinus in the larynx.


The cyst wall is composed of squamous epithelium (90%), columnar cells with or without cilia, or a mixture of both with lymphoid infiltrate, often with prominent germinal centers and few subcapsular lymph sinuses. Cholesterol crystals may be found in the fluid extracted from a branchial cyst.


Tooth paste like material rich in cholesterol.

Clinical features:

  1. Age: Late childhood and young adults M=F.
  2. Branchial cleft cysts are often asymptomatic.
  3. May be painful only if infected.
  4. Characteristics of Branchial cyst:
    • Smooth, ovoid in size.
    • Fluctuation positive.
    • Transillumination negative.
    • Non compressible.
    • Non palpable cervical lymph nodes.
  5. The location of the branchial cleft cyst differs according to the type:
    • A 1st branchial cleft cyst is typically smooth, non-tender, fluctuant mass found between the external auditory canal and submandibular area and frequently will have a cutaneous punctum from which fluid may be expressed. It is variably involved with the parotid gland and facial nerve.
    • A 2nd branchial cleft cyst is typically identified by a pit or punctum of the skin at the lower anterior border of the sternocleidomastoid. It may connect to the tonsillar fossa of the pharynx. It can be related to the glossopharyngeal and hypoglossal nerve as well as carotid vessels. If secondarily infected, the cyst can be tender and in severe cases may lead to airway compromise. Discharge may be present on the skin or into the pharynx as it can be associated with a sinus tract.
    • 3rd and 4th branchial cleft cysts are rare. They are normally present on the left side of the neck or the suprasternal notch/clavicular area and present as a firm mass or infected cyst draining to the piriform sinus or external neck skin. Fistulae are more likely to present when infected or repeated incision and drainage procedures due to recurrence.

Diagnostic Criteria:

  1. Diagnosis of branchial cleft cysts are typically done clinically due to their relatively consistent location in the neck.
  2. Cholesterol crystals present in aspirated material.
  3. Imaging studies includes:
    • A sinogram can be obtained by injecting radiopaque dye in the sinus tract to delineate the course and determine the size of the cyst.
    • Ultrasonography is done 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.
  4. Fine-needle aspiration is helpful to distinguish a branchial cleft cyst from malignant neoplasm.


  1. The treatment of a branchial cleft cyst is elective excision due to
    • Risk of infection.
    • Enlargement.
    • Risk of malignancy (though very low).
  2. Excision of the cyst

    a) The incision is planned to optimize cosmesis, placing it within a natural skin crease. Methylene blue can be used by dipping a lacrimal probe in the solution and inserting it into the tract to make it easier to identify intraoperatively. Dissection should be performed carefully over the surface of the lesion as the tract can be thin-walled. If the track is long, then exposure should be obtained by using a second “stepladder” incision placed within a skin crease cephalic to the primary incision. During dissection one must avoid injury to external and internal carotid arteries, pharyngeal wall, accessory and hypoglossal nerves.

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Differential diagnosis:

  • Tuberculous lymphadenitis.
  • Reactive lymphadenopathy.
  • Lymphoma.
  • Nerve sheath tumor.
  • In children, dermoid cyst or rhabdomyosarcoma should also be considered.


  1. Recurrent infection.
  2. Abscess formation.
  3. Scar formation due to recurrent infection and abscess formation.
  4. Once branchial cleft cysts are excised, recurrence is relatively uncommon. However, if previous surgery or recurrent infection has occurred, recurrence can be as high as 20%.

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