Back To Search Results

Branchial Cleft Cyst

Editor: Carl Shermetaro Updated: 6/30/2023 12:39:57 PM


Branchial cleft cysts are congenital anomalies arising from the first through fourth pharyngeal clefts. The most common type of branchial cleft cyst arises from the second cleft, with anomalies derived from the first, third, and fourth clefts being rarer. As this is a congenital anomaly, it is present at birth, though it may not be obvious or symptomatic until later. The majority of lesions present in childhood as a visible punctum on the skin though they may present as cysts or neck masses, occasionally mistaken for neck abscesses. Branchial cleft anomalies present in one of three forms: cysts, sinuses, or fistulae. Cysts have an epithelial lining without external openings, and as such, may be asymptomatic and only noticed incidentally. Such cysts may not present until adulthood. Sinus tracts may communicate either externally with skin as a visible punctum or internally with the pharynx or larynx, where the punctate opening will be visible only on endoscopy. Branchial cleft fistulae are true communications connecting the pharynx or larynx with the external skin.[1][2][3][4][5]


Register For Free And Read The Full Article
Get the answers you need instantly with the StatPearls Clinical Decision Support tool. StatPearls spent the last decade developing the largest and most updated Point-of Care resource ever developed. Earn CME/CE by searching and reading articles.
  • Dropdown arrow Search engine and full access to all medical articles
  • Dropdown arrow 10 free questions in your specialty
  • Dropdown arrow Free CME/CE Activities
  • Dropdown arrow Free daily question in your email
  • Dropdown arrow Save favorite articles to your dashboard
  • Dropdown arrow Emails offering discounts

Learn more about a Subscription to StatPearls Point-of-Care


Branchial cleft anomalies form due to the incomplete involution of branchial cleft structures. Around the fourth 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, with the arches are separated by depressions known as clefts on the ectodermal surface and corresponding pouches on the endodermal surface, yielding four pharyngeal clefts. The second arch develops caudally and then covers the third and fourth 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.[6][7][8][9]

  • First Branchial Cleft Cyst
    • First cleft cysts make up approximately 5% to 25% of all branchial cleft anomalies and are 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 (57%), deep (30%), or between (13%) branches of the facial nerve.[10]
  • Second 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 second branchial cleft cysts can be associated with branchio-oto-renal syndrome. The course of a second branchial cleft sinus is as follows: the external opening is located on the neck skin as described above, with the fistula traveling deep to platysma then passing in between the internal and external carotids, coursing superficial to both glossopharyngeal and hypoglossal nerves before connecting to the tonsillar fossa. Cysts or sinuses of the second branchial cleft can exist anywhere along this course.[11][12]
  • Third Branchial Cleft Cyst
    • Third 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 third branchial cleft sinus course is as follows: from the skin opening described above, the tract courses deep to platysma and course posterior to the internal carotid artery. It will pass between the glossopharyngeal and hypoglossal nerves and may be intimately associated with the superior laryngeal nerve (classically coursing superior to it). It then connects to the pyriform sinus in the larynx.[13]
  • Fourth Branchial Cleft Cyst
    • Fourth 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 exact course of the fourth branchial cleft remnant is not as well characterized owing to its rarity. However, 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). These run superficial to the recurrent laryngeal nerve and hypoglossal nerve, terminating in the apex of the pyriform sinus in the larynx.[13]


The true incidence of branchial cleft anomalies in the United States is unknown despite their relative frequency. This is likely due to the variety of both the anomalies and their presentations complicating accurate reporting. There is no ethnic or gender predilection. Most branchial cleft anomalies arise from the second pouch, while the first, third, and fourth pouches are rare, and 10% of branchial cleft anomalies are bilateral. These typically present in the first decade of life, but if no external communication is present, the presentation may be delayed into adulthood.[5]


Branchial cleft cysts are embryologic anomalies 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-oculofacial (BOF) syndromes should be suspected when a patient presents with preauricular pits or multiple branchial cleft anomalies, including bilateral anomalies. These syndromes are autosomal dominant conditions associated with hearing loss, ear malformations, and renal anomalies in the BOR syndrome. At the same time, BOF includes eye anomalies, such as microphthalmia and obstructed lacrimal ducts, and facial anomalies, such as cleft lip and palate.[5]


Branchial cleft cysts are lined with stratified squamous epithelium and may contain keratinous debris inside the cyst. In some cases, the cyst wall is lined by ciliated columnar epithelium resulting in more mucoid contents. 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.[5]

History and Physical

Branchial cleft cysts are often asymptomatic but can often become tender, enlarged, or inflamed with superinfection or abscess formation during episodes of upper respiratory tract infections. The patient can present with purulent drainage of the sinus to the skin or pharynx in such situations. The most concerning symptoms include dysphagia, dyspnea, and stridor due to cyst compression of the upper airway.[14] 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 sternocleidomastoid muscle. However, they may present with acute infection. Change in size during upper respiratory infections is noted in up to 25%. 

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

  • A first branchial cleft cyst is typically smooth, non-tender, fluctuant mass found between the external auditory canal and submandibular area. Frequently, it will have a cutaneous punctum from which fluid may be expressed. It is variably involved with the parotid gland and facial nerve, and there may be a connection to the middle or external ear, so an otologic exam is crucial in these patients.[15]
  • A second 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 in proximity to the glossopharyngeal and hypoglossal nerve as well as carotid vessels. The cysts are tender if secondarily infected, and in severe cases, may lead to airway compromise. If it is associated with a sinus tract, a mucoid or purulent discharge may be present on the skin or into the pharynx.[16][17]
  • 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 or external neck skin. These fistulae are more likely to present when infected and they may have undergone repeated incision and drainage procedures owing to incorrect diagnosis and subsequent recurrence.[18]


There is no specific laboratory test needed for evaluation.[17][19][20]

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.[1][19]
  • Contrast-enhanced CT will depict a cystic and enhanced mass in the neck.[20]
  • MRI can be used for a finer resolution.[21]

Fine-needle aspiration is helpful to distinguish a branchial cleft cyst from a malignant neoplasm.[16]

Treatment / Management

The treatment of a branchial cleft cyst is elective excision due to the risk of infection, further enlargement, or extremely low risk of malignancy. So long as there is no airway compromise or frank abscess, there is typically no urgency; clinicians can defer excision beyond 3 to 6 months of age or allow treatment of an acute infection.[5] However, in the event of airway compromise or large abscess, emergent surgery may be required.[22][23] Systemic antibiotics and aspiration are generally preferable to incision and drainage, which might produce more distortion of the surgical planes.[24](B2)

The incision is planned to optimize cosmesis, placing it within a natural skin crease whenever possible. If a fistula or sinus is present, then identifying the tract by gentle insertion of a probe or catheter is important in order to ensure complete excision and decrease the chance of recurrence. 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 cephalad to the primary incision. In first branchial cleft cysts, initial exposure of the main trunk of the facial nerve and branches should be performed with a superficial parotidectomy approach to reduce the risk of facial nerve injury, as the anomaly can be intimately associated with the nerve. Preoperative fistulograms can also be useful.[9][25] In the event that a patient cannot undergo surgery, ethanol ablation has been used as an alternative in this patient population, though it is not usually recommended as a primary treatment.[9][26]

Third and fourth branchial cleft cysts are treated with a standard transverse cervical incision to identify the recurrent laryngeal nerves, occasionally requiring thyroid lobectomy to completely excise the tract to the piriform sinus. Before the trans-cervical portion of the surgery is begun, direct laryngoscopy is performed to confirm the diagnosis and to allow endoscopic cannulation of the opening into the piriform sinus to facilitate dissection during excision.[5][27]

Differential Diagnosis

Differentials include:[1]

  • Lymphadenopathy
  • Hemangioma
  • Carotid body tumor
  • Cystic hygroma
  • Ectopic thyroid/salivary tissue
  • Vascular neoplasm/malformation
  • Thyroglossal duct cysts
  • Cat scratch disease
  • Atypical mycobacterial infections
  • Cystic squamous cell carcinoma


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%.[5]


An otolaryngologist or pediatric otolaryngologist should be consulted in these cases depending on the age of the patient.

Deterrence and Patient Education

Branchial cleft anomalies are congenital malformations, and currently, there are no preventative measures to reduce the likelihood of presentation. Patients and physicians should be educated on the symptomatology and physical exam findings that could lead to the early diagnosis of these lesions. This could reduce the cost of care for the patient, which would otherwise consist of future physician visits, multiple courses of antibiotics, and diagnostic imaging.

Enhancing Healthcare Team Outcomes

The management of patients with branchial cleft cysts is interprofessional. The surgery is usually performed by an otolaryngologist or, rarely, by a pediatric surgeon. However, the follow-up may be required by a nurse practitioner, pediatrician, or primary care provider. Surgery is the only treatment for branchial cleft cysts. Two well-known complications are recurrence and infection. Specialty trained nurses in the fields of otolaryngology are involved in family education, patient monitoring, and patient feedback. In rare cases, injury to the facial nerves may also occur, requiring further surgery. The outcomes after branchial cleft cysts are excellent, with a recurrence rate of about 3% to 7% (Level V).[24][25]



Patel S, Bhatt AA. Thyroglossal duct pathology and mimics. Insights into imaging. 2019 Feb 6:10(1):12. doi: 10.1186/s13244-019-0694-x. Epub 2019 Feb 6     [PubMed PMID: 30725193]


Bahakim A, Francois M, Van Den Abbeele T. Congenital Midline Cervical Cleft and W-Plasty: Our Experience. International journal of otolaryngology. 2018:2018():5081540. doi: 10.1155/2018/5081540. Epub 2018 Dec 2     [PubMed PMID: 30627168]


Banakis Hartl RM, Said S, Mann SE. Bilateral Ear Canal Cholesteatoma with Underlying Type I First Branchial Cleft Anomalies. The Annals of otology, rhinology, and laryngology. 2019 Apr:128(4):360-364. doi: 10.1177/0003489418821700. Epub 2019 Jan 4     [PubMed PMID: 30607978]


Meng F, Zhu Z, Ord RA, Zhang T. A unique location of branchial cleft cyst: case report and review of the literature. International journal of oral and maxillofacial surgery. 2019 Jun:48(6):712-715. doi: 10.1016/j.ijom.2018.11.014. Epub 2018 Dec 20     [PubMed PMID: 30579743]

Level 3 (low-level) evidence


Prosser JD, Myer CM 3rd. Branchial cleft anomalies and thymic cysts. Otolaryngologic clinics of North America. 2015 Feb:48(1):1-14     [PubMed PMID: 25442127]


Tazegul G, Bozoğlan H, Doğan Ö, Sari R, Altunbaş HA, Balci MK. Cystic lateral neck mass: Thyroid carcinoma metastasis to branchial cleft cyst. Journal of cancer research and therapeutics. 2018 Oct-Dec:14(6):1437-1438. doi: 10.4103/0973-1482.188440. Epub     [PubMed PMID: 30488872]


Oh JH, Chang YW, Lee EJ. Sonographic diagnosis of coexisting ectopic thyroid and fourth branchial cleft cyst. Journal of clinical ultrasound : JCU. 2018 Nov:46(9):582-584. doi: 10.1002/jcu.22630. Epub 2018 Oct 4     [PubMed PMID: 30288756]


Williams DS. Neck Mass in a Five-year-old Afghan Child. Journal of insurance medicine (New York, N.Y.). 2018 Jan:47(3):191-193. doi: 10.17849/insm-47-03-191-193.1. Epub     [PubMed PMID: 30192721]


Koch EM, Fazel A, Hoffmann M. Cystic masses of the lateral neck - Proposition of an algorithm for increased treatment efficiency. Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery. 2018 Sep:46(9):1664-1668. doi: 10.1016/j.jcms.2018.06.004. Epub 2018 Jun 12     [PubMed PMID: 29983308]


Work WP. Newer concepts of first branchial cleft defects. The Laryngoscope. 1972 Sep:82(9):1581-93     [PubMed PMID: 5079586]


Bajaj Y, Ifeacho S, Tweedie D, Jephson CG, Albert DM, Cochrane LA, Wyatt ME, Jonas N, Hartley BE. Branchial anomalies in children. International journal of pediatric otorhinolaryngology. 2011 Aug:75(8):1020-3. doi: 10.1016/j.ijporl.2011.05.008. Epub 2011 Jun 15     [PubMed PMID: 21680029]

Level 2 (mid-level) evidence


Muller S, Aiken A, Magliocca K, Chen AY. Second Branchial Cleft Cyst. Head and neck pathology. 2015 Sep:9(3):379-83. doi: 10.1007/s12105-014-0592-y. Epub 2014 Nov 25     [PubMed PMID: 25421295]

Level 3 (low-level) evidence


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:44(7):1432-9. doi: 10.1016/j.jpedsurg.2008.12.001. Epub     [PubMed PMID: 19573674]

Level 3 (low-level) evidence


Possel L, François M, Van den Abbeele T, Narcy P. [Mode of presentation of fistula of the first branchial cleft]. Archives de pediatrie : organe officiel de la Societe francaise de pediatrie. 1997 Nov:4(11):1087-92     [PubMed PMID: 9488742]


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:19(19):873-4     [PubMed PMID: 16419954]

Level 3 (low-level) evidence


Shen LF, Zhou SH, Chen QQ, Yu Q. Second branchial cleft anomalies in children: a literature review. Pediatric surgery international. 2018 Dec:34(12):1251-1256. doi: 10.1007/s00383-018-4348-8. Epub 2018 Sep 24     [PubMed PMID: 30251021]


Lee DH, Yoon TM, Lee JK, Lim SC. Clinical Study of Second Branchial Cleft Anomalies. The Journal of craniofacial surgery. 2018 Sep:29(6):e557-e560. doi: 10.1097/SCS.0000000000004540. Epub     [PubMed PMID: 29608472]


Quintanilla-Dieck L, Penn EB Jr. Congenital Neck Masses. Clinics in perinatology. 2018 Dec:45(4):769-785. doi: 10.1016/j.clp.2018.07.012. Epub 2018 Sep 18     [PubMed PMID: 30396417]


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:38(4):1239-1263. doi: 10.1148/rg.2018170165. Epub     [PubMed PMID: 29995618]


Friedman E, Patiño MO, Udayasankar UK. Imaging of Pediatric Salivary Glands. Neuroimaging clinics of North America. 2018 May:28(2):209-226. doi: 10.1016/j.nic.2018.01.005. Epub 2018 Mar 7     [PubMed PMID: 29622115]


Brown RE, Harave S. Diagnostic imaging of benign and malignant neck masses in children-a pictorial review. Quantitative imaging in medicine and surgery. 2016 Oct:6(5):591-604     [PubMed PMID: 27942480]


Prada LR, Koripalli VS, Merino CL, Fulger I. A Case of a Rapidly Enlarging Neck Mass with Airway Compromise. Journal of clinical and diagnostic research : JCDR. 2017 May:11(5):OD14-OD16. doi: 10.7860/JCDR/2017/25685.9874. Epub 2017 May 1     [PubMed PMID: 28658834]

Level 3 (low-level) evidence


Schmidt K, Leal A, McGill T, Jacob R. Rapidly enlarging neck mass in a neonate causing airway compromise. Proceedings (Baylor University. Medical Center). 2016 Apr:29(2):183-4     [PubMed PMID: 27034563]


Mattioni J, Azari S, Hoover T, Weaver D, Chennupati SK. A cross-sectional evaluation of outcomes of pediatric branchial cleft cyst excision. International journal of pediatric otorhinolaryngology. 2019 Apr:119():171-176. doi: 10.1016/j.ijporl.2019.01.030. Epub 2019 Jan 23     [PubMed PMID: 30735909]

Level 2 (mid-level) evidence


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:75(6):1209-1215. doi: 10.1016/j.joms.2016.12.008. Epub 2016 Dec 15     [PubMed PMID: 28061361]


Ha EJ, Baek SM, Baek JH, Shin SY, Han M, Kim CH. Efficacy and Safety of Ethanol Ablation for Branchial Cleft Cysts. AJNR. American journal of neuroradiology. 2017 Dec:38(12):2351-2356. doi: 10.3174/ajnr.A5373. Epub 2017 Sep 28     [PubMed PMID: 28970243]


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:126(6):1339-42. doi: 10.1002/lary.25711. Epub 2015 Oct 15     [PubMed PMID: 26466762]