Path Image

A thin layer of epithelium overlies a brisk chronic inflammatory reaction and fibrosis in the wall of the cyst.

The underlying lymphoid infiltrate is quite robust and can occasionally form germinal centers (although that is not seen here). This combination of a lymphoid stroma and epithelial-lined cysts is the reason for its alternative alias - lymphoepithelial cyst.

A stratified squamous lining as seen here is by far the most common type of lining. Respiratory epithelium may occasionally be encountered, or a mixture of both.

This different case shows a lining which is not squamous.

On higher power it appears to represent respiratory epithelium. Some secondary reactive changes are also present.

This chart demonstrates the different derivatives of the first four pharyngeal arches. Understanding what structures form from each arch is important for determining the type of branchial cleft and the position of a tract if present.


The branchial (pharyngeal) apparatus in humans is the progenitor of many head and neck structures, and of the six branchial arches, the first four are the most important. Branchial (pharyngeal) arches are composed of a bar of mesoderm lined externally by ectoderm and internally by endoderm.

In addition to a cartilaginous core, each arch has an aortic arch derivative, and a definite cranial nerve. These cranial nerves will supply the structures that develop from the arch.

On the external surface, the identations between the arches are called branchial clefts or grooves. The equivalent structure inside the fetus are called branchial pouches. In other words, the outpouchings of the foregut lie directly opposite of the indentation of the branchial groove.

When a branchial cleft is not properly involuted during development, the remnant forms an epithelium-lined cyst that may connect to the overlying skin via a sinus tract. Rarely, both the branchial pouch and branchial cleft fail to involute, and a more extensive communication may form. For example, if this occurred in the 1st branchial groove and pouch, there would be a fistula between the pharynx and skin (Branstetter).

Histologically, the cysts are lined by squamous and occasionally respiratory epithelium. There is often an robust underlying lymphoid infiltrate; germinal centers may even be seen on occasion. This is why branchial cysts are also called lymphoepithelial cysts. The cystic contents may be serous, mucinous or contain debris (desquamated cells) (Kumar).

It is important to recognize this entity and not confuse it with metastatic lymph node (i.e. containing squamous cell carcinoma). Note that branchial cleft cysts that undergo malignant transformation do exist, but are exceptionally rare (Rosai).


Branchial cysts, tracts, and sinuses have been reported for all of the first four branchial (pharyngeal) arches. The location will depend on the specific branchial cleft involved.

For example, first pouch remnants are located in the preauricular area or beneath the posterior aspect of the mandible (and may be connected to the auditory canal). Second pouch remnants appear anterior to the sternocleidomastoid and may communicate with the pharynx. Third and fourth pouch remnants are usually located in the suprasternal or supraclavicular region (Rosai).


Surgical excision is typically the treatment of choice. There are a variety of procedures designed to excise the complete branchial remnant.


Complete excision of the retained epithelium is necessary to prevent cyst re-accumulation. Additionally, if there are pharyngeal or skin openings the cyst tracts, these must also be addressed to prevent recurrence.


Branstetter BF. Branchial Cleft Cysts: eMedicine. Last updated March 11th 2009. Available at:

Kumar V, Abbas AK, Fausto N. Robbins and Cotran Pathologic Basis of Disease. 7th Ed. Philadelphia, PA: Elsevier; 2005: 788-9.

Rosai, J. Rosai and Ackerman's Surgical Pathology. 9th Ed. Philadelphia, PA: Elsevier; 2004: 518-519.

Last updated: 2010-12-06
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