Branchial Cleft Cysts

Earn CME/CE in your profession:

Continuing Education Activity

Branchial cleft cysts are congenital epithelial cysts that comprise approximately one-third of congenital neck masses. They are benign lesions and can present at any age. They typically present after an upper respiratory tract infection as a waxing and waning neck mass that parallels the course of the illness. This activity explains the pathophysiology, evaluation, and management of patients with branchial cleft cysts. It highlights the role of the interprofessional team in treating and decreasing morbidity in patients with branchial cleft cysts.


  • Describe the pathophysiology, epidemiology, and clinical presentations of patients with branchial cleft cysts.
  • Outline the evaluation in a patient with branchial cleft cysts.
  • Explain the management strategies in a patient with branchial cleft cysts.
  • Explain the importance of a cohesive, interprofessional team approach to caring for patients with branchial cleft cysts.


Branchial cleft cysts are congenital epithelial cysts that comprise approximately one-third of congenital neck masses. They are benign lesions and can present at any age. The majority are second branchial cleft cysts and appear as a non-tender fluctuant mass along the anterior border of the sternocleidomastoid muscle. They typically present after an upper respiratory tract infection as a waxing and waning neck mass that parallels the course of the illness.[1][2]


Branchial cleft cysts result from elements of the cervical sinus of His becoming entrapped without an external or internal opening, forming an epithelial lined cyst. They have also been proposed to develop from epithelial rests of tissue from Waldeyer’s ring. Pure branchial cleft cysts/sinuses are relatively rare, and often there is a combination of the 2.[3][4]


Branchial cleft cysts develop early during gestation. During week 4 of embryonic development, four branchial (pharyngeal) clefts form five ridges. These ridges contribute to the formation of portions of the head, neck, and thorax. These mesodermal ridges form the 6 branchial (pharyngeal) arches. The branchial arches form grooves or clefts externally and pouch internally. A pouch is associated with a ventral or dorsal wing and is lined by endoderm. The branchial arch derivatives are lined with mesoderm. Ectoderm lines the branchial cleft derivatives. Each arch is associated with a cartilaginous bar, carotid artery derivative,  cranial nerve, and vein. The nerves run anterior to the artery associated with each arch, except for in the case of the sixth arch where the nerve runs posterior to the artery.

The first branchial arch also known as the mandibular arch is associated with the trigeminal (V) nerve while the artery degenerates. The second arch is associated with the facial (VII) nerve and the second aortic arch degenerates. If this artery does not degenerate, then a stapedial artery persists. The third branchial arch is associated with cranial nerve IX, the glossopharyngeal nerve. The common and internal carotid arteries are associated with the third arch. The fourth arch is associated with the superior laryngeal nerve, a branch of the vagus (X) nerve. On the left, the fourth arch gives rise to the aorta, while on the right the fourth arch gives rise to the proximal subclavian artery. The fifth branchial arch degenerates. The sixth branchial arch gives rise to the pulmonary artery on both the left and right in addition the ductus arteriosus on the left. The sixth arch also gives rise to a branch of the vagus (X) nerve, the recurrent laryngeal nerve. The 12th cranial nerve lies caudal to all arches.


Branchial cleft cysts are the most frequent cause of congenital neck masses, comprising approximately one-third of all congenital neck masses. They are the most common lateral neck mass, with 2% to 3% occurring bilaterally. While they occur more frequently in patients with a family history, there is no reported predilection for gender or race. They are more commonly found during childhood but can be seen in adults.[5]


Branchial cleft cysts represent incomplete involution of branchial cleft structures. A branchial cleft cyst has no opening in the skin or digestive tract. A branchial cleft sinus has a single opening to the skin or digestive tract versus a branchial cleft fistula which has an opening to skin and digestive tract. Stratified squamous epithelium lines branchial cleft cysts in 90% of cases.


The majority of branchial cleft cysts are lined with stratified squamous epithelium. The inside of the cyst may reveal a keratinous plug. In rare cases, the cyst may be lined with ciliated columnar epithelium. If infected, an inflammatory infiltrate may be present.

History and Physical

A branchial cleft cyst is typically present as a non-tender, fluctuant, lateral neck mass. They may become inflamed, tender and possibly suppurate during an upper respiratory tract infection.

Specific Features of Each Level of Cyst

First Branchial Cleft Cyst

First branchial cleft cysts comprise 5% to 25% of all branchial cleft cysts. There are two different subtypes within the first branchial cleft category. A Work’s type I first branchial cleft cyst presents as a preauricular cyst. There is a duplication of the external auditory canal which is comprised of ectodermal elements only. The tract of the type I cleft passes lateral to cranial nerve VII, parallels the external auditory canal and ends in the mesotympanum. A Work’s type II branchial cleft cyst is found along the angle of the mandible, periauricular area or in the submandibular area. Type II first branchial clefts are more common and contain both ectoderm and mesoderm. Fifty-seven percent of type II first branchial cleft cysts pass laterally to cranial nerve VII, while 30% of them pass medially. These cysts end within or near the external auditory canal.

Second Branchial Cleft Cyst

Second branchial cleft cysts are the most common type and have been reported to comprise up to 95% of all branchial cleft cysts. Second branchial cleft cysts run between internal and external carotid arteries, pass deep to cranial nerve VII, superficial to cranial nerves XII and IX, and end internally in the tonsillar fossa if there is an associated sinus. They run deep to second arch derivatives such as the manubrium of the malleus, the long process of the incus and the stapes superstructure and superficial to third arch derivatives such as the greater cornu of the hyoid.

Third Branchial Cleft Cyst

A third branchial cleft cyst is more commonly found on the left side in the lower portion of the anterior neck. These cysts may present as an abscess, neck mass or thyroiditis. Third branchial cleft cysts run superficially to cranial nerve X and the common carotid artery, superficial to cranial nerve XII and deep to cranial nerve IX. The associated tract, if present, then passes through the thyrohyoid membrane above superior laryngeal nerve and opens into the upper piriform sinus.

Fourth Branchial Cleft Cyst

These branchial cleft cysts are rare. A fourth branchial cleft cyst typically presents as a low anterior neck mass, beneath the platysma and anterior to the sternocleidomastoid muscle. The tract of a fourth branchial cleft cysts loops around cranial nerve XII then runs posterior to the common carotid artery and thyroid following the recurrent branch of cranial nerve X. It then runs through the cricothyroid membrane below superior laryngeal nerve with recurrent laryngeal nerve deep to its path and drains into the apex of the piriform sinus.


Various imaging modalities have been used to evaluate for the presence of a branchial cleft cyst. Three commonly used techniques are ultrasound, computed tomography (CT) scanning, and magnetic resonance imaging (MRI). Larger cystic lesions can be seen with ultrasound. A CT with contrast will also show a cystic appearing, well circumscribed, enhancing lesion. CT imaging can also assist with identification of structures both deep and superficial to the lesion to better categorize the type of branchial cleft cyst. MRI with gadolinium may show a (KA21) branchial cleft with wall enhancement. MRI is typically better for evaluation of type II first branchial cleft cyst because it provides for better evaluation of the parotid gland and involvement of surrounding neural structures.[6]

Treatment / Management

Treatment of a branchial cleft cyst is complete surgical excision. If a cyst is found during an infection, the surgeon should allow adequate time for the infection to resolve before scheduling the procedure. Incision and drainage should be avoided if possible as it can make definitive excision more difficult. For treatment of third and fourth branchial cleft cysts, a partial thyroidectomy may be required. Direct laryngoscopy with visualization of any opening in the pyriform sinus can aid in localization of tract. Some consider cautery of pyriform sinus tract alone as adequate for treatment of third and fourth branchial cleft cysts.[1]

Differential Diagnosis

  • Hemangioma
  • Ectopic thyroid or salivary gland tissue
  • Lymphadenopathy


  • Infection
  • Abscess formation
  • Damage to adjacent nerves during excision

Pearls and Other Issues

Branchial cleft cysts are the most typical congenital neck masses. Typically, they present as a non-tender, fluctuant mass along the anterior border of the sternocleidomastoid muscle. These cysts may present more commonly during or after an upper respiratory tract infection. While there are four different types of branchial cleft cysts described, second branchial cleft cysts are most common. It is important for providers to consider branchial cleft cysts in the differential diagnosis of a neck mass in both children and adults. Treatment is surgical excision after the acute infection has been adequately treated.

Enhancing Healthcare Team Outcomes

Branchial cleft cysts are usually managed by a head and neck or general surgeon. But since most of these lesions occur in young children, the nurse can play a vital role in education of the public. The parents have to be told that these lesions are benign and usually cause no complications. However, if surgery is undertaken, the child should be followed up to ensure that there is no recurrence. The nurse should educate the parent on symptoms of recurrence and when to seek medical help. [7][8](Level V)


The majority of branchial cleft cysts are asymptomatic. The few that become inflamed or infected may present with pain, sinus tracks or fluctuant abscess. Spontaneous rupture of a cyst is not uncommon. The small cysts usually do not cause symptoms but larger ones, depending on their location may cause dysphagia, dyspnea or stridor. When surgically excised, recurrence is rare. However, if the wall of the cyst is not excised, recurrence rates of 10-20% have been reported.[9][10] (Level V)

Article Details

Article Author

Samantha Allen

Article Author

Zohaib Jamal

Article Editor:

Julie Goldman


7/21/2021 11:31:40 PM

PubMed Link:

Branchial Cleft Cysts



Cystic masses of the lateral neck - Proposition of an algorithm for increased treatment efficiency., Koch EM,Fazel A,Hoffmann M,, Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery, 2018 Jun 12     [PubMed PMID: 29983308]


Cyst, Branchial Cleft, Coste AH,Shermetaro C,,, 2018 Jan     [PubMed PMID: 29763089]


Clinical Study of Second Branchial Cleft Anomalies., Lee DH,Yoon TM,Lee JK,Lim SC,, The Journal of craniofacial surgery, 2018 Mar 30     [PubMed PMID: 29608472]


Branchial Cleft Cysts, Allen SB,Goldman J,,, 2018 Jan     [PubMed PMID: 29494074]


Teo NW,Ibrahim SI,Tan KK, Distribution of branchial anomalies in a paediatric Asian population. Singapore medical journal. 2015 Apr     [PubMed PMID: 25917471]


Bansal AG,Oudsema R,Masseaux JA,Rosenberg HK, US of Pediatric Superficial Masses of the Head and Neck. Radiographics : a review publication of the Radiological Society of North America, Inc. 2018 Jul-Aug     [PubMed PMID: 29995618]


Nicoucar K,Giger R,Pope HG Jr,Jaecklin T,Dulguerov P, Management of congenital fourth branchial arch anomalies: a review and analysis of published cases. Journal of pediatric surgery. 2009 Jul     [PubMed PMID: 19573674]


Xiao H,Kong W,Gong S,Wang J,Liu S,Shi H, [Surgical treatment of first branchial cleft anomaly]. Lin chuang er bi yan hou ke za zhi = Journal of clinical otorhinolaryngology. 2005 Oct     [PubMed PMID: 16419954]


Ahn D,Lee GJ,Sohn JH, Comparison of the Retroauricular Approach and Transcervical Approach for Excision of a Second Brachial Cleft Cyst. Journal of oral and maxillofacial surgery : official journal of the American Association of Oral and Maxillofacial Surgeons. 2017 Jun     [PubMed PMID: 28061361]


Teng SE,Paul BC,Brumm JD,Fritz M,Fang Y,Myssiorek D, Endoscope-assisted approach to excision of branchial cleft cysts. The Laryngoscope. 2016 Jun     [PubMed PMID: 26466762]