Branchial Cleft Fistula – Causes, Symptoms, Diagnosis, Treatment and Ongoing care



  • A congenital, abnormal tract connecting the skin of the neck with an internal structure, resulting from failure of closure of 1 of the 4 branchial clefts
  • May involve branchial clefts I–IV, which develop in the 4th gestational week
  • System(s) affected: Skin/Exocrine

Pediatric Considerations

Almost all occur in the pediatric age group.


  • Predominant age: By definition, all are present at birth, although they may remain unnoticed for some time. (Branchial cleft cysts may not present until later childhood.) (1)[C]
  • Predominant sex: Unknown





Risk Factors

Positive family history


10% have family history.


  • Both respiratory and squamous epithelium alone or in combination may line branchial anomalies (2)[C].
  • Squamous epithelium is found more commonly in cysts.
  • Ciliated, columnar epithelium is found more commonly in sinuses and fistulae.


  • The 1st branchial cleft contributes to the tympanic cavity and eustachian tube. Related fistulae are very rare and tend to be infra- or retroauricular. (Preauricular cysts and sinuses are not thought to be of branchial cleft origin.) The first branchial cleft anomalies enter the external auditory canal and/or the middle ear
  • The 2nd branchial cleft forms the hyoid bone and tonsillar fossa. Related fistulae (most common variant) course between the internal and external carotid arteries. Internal opening usually at level of tonsillar fossa. External opening along anterior border of sternocleidomastoid muscle (1)[C]. 2nd branchial cleft lesions represent 90% or more of all branchial cleft lesions.
  • 3rd and 4th branchial clefts form parathyroid glands, thymus, and portions of thyroid (parafollicular cells). Fistulae are rare; those from third cleft course posterior to carotid artery; both should have external ostia on lower anterior neck. Sinus tracts (also called pyriform sinuses) originate in the pyriform sinus and course adjacent to the thyroid cartilage (3)[C]. 3rd branchial cleft anomalies represent 2–8% of all branchial anomalies.

Commonly Associated Conditions

Microtia and aural atresia occur with failure of development of 1st branchial cleft.

Surgery, Cleft lip and palate, Branchial Cleft Fistula, external carotid arteries, external auditory canal, sinus tracts, tympanic cavity,



  • History of drainage from cervical area
  • Neck abscess or suppurative thyroiditis

Physical Exam

  • Presence of tiny external opening usually on mid-to-lower neck along anterior border of sternocleidomastoid muscle
  • Spontaneous mucoid drainage
  • External openings may also be marked by a skin tag or cartilage.
  • Infection may rarely be the presenting sign, with erythema, swelling, pain, or fever.
  • 10% are bilateral.
  • Small orifices located in the mid-neck, most commonly along the anterior border of the sternocleidomastoid muscle (less commonly in the lower neck or postauricular)
  • Third branchial cleft anomalies are predominantly left-sided (89%) (4)[B].

Diagnostic Tests & Interpretation


Support's development and hosting

Culture if signs of infection


  • Computed tomography (CT) of neck with IV contrast occasionally beneficial in 3rd and 4th branchial cleft fistulas/sinus (3)[C].
  • CT may demonstrate fistula tract in up to 64% of cases (2)[C].
  • Magnetic resonance imaging and ultrasound may occasionally be useful.
  • Barium esophagogram may demonstrate the fistula (may have a sensitivity rate of 50–80% when used to evaluate 3rd and 4th branchial anomalies (2)[C].

Diagnostic Procedures/Surgery

  • Sinogram or fistulogram may be done, but is of little value.
  • Pharyngoscopy may occasionally be useful.

Pathological Findings

  • Lined by stratified squamous epithelium; may contain hair follicles, sweat glands, sebaceous glands, or cartilage
  • Some are lined by ciliated columnar epithelium.

Differential Diagnosis

  • External sinuses
  • Cystic hygroma
  • Dermoid cysts
  • Lymphadenopathy


  • Surgical excision
  • Outpatient status usually appropriate

Surgery/Other Procedures

  • Small transverse incision at external ostium with careful dissection of fistula (1)[C]
  • Stepladder incisions may be needed.
  • End of fistula ligated flush with pharyngeal mucosa. 1st branchial cleft lesions may require larger incision (1)[C].
  • Methylene blue injection into fistula may be useful.
  • Drains are not used.
  • Antibiotics only for infection
  • Patients with abscess related to 3rd branchial cleft anomalies frequently require initial incision and drainage (4)[B]:
    • Incision and drainage failure rate of 94% at 1st attempt
    • Virtually all require resection.
    • Those with acute suppurative thyroiditis may require partial thyroidectomy with resection.
  • Endoscopic cauterization of the internal orifice has been successfully used in some cases.

Ongoing Care

Follow-Up Recommendations

Patient Monitoring

  • Follow at weekly intervals if infected until resolution, then excision
  • Postoperative visit at 2 weeks




  • Facial nerve injury
  • Hypoglossal nerve injury
  • Spinal accessory nerve injury
  • Vagus nerve injury
  • Infection
  • Carotid artery injury
  • Possible recurrence if any epithelium remains
  • Neoplastic degeneration of branchial remnants (about 250 reported cases) if not resected


1. Roback SA, Telander RL. Thyroglossal duct cysts and branchial cleft anomalies. Sem Ped Surg. 1994;3:142–46.

2. Waldhausen JH et al. Branchial cleft and arch anomalies in children. Semin Pediatr Surg. 2006;15:64–9.

3. Liberman M, Kay S, Emil S, et al. Ten years of experience with third and fourth branchial remnants. J Ped Surg. 2002;37:685–90.

4. Nicoucar K, Giger R, Jaecklin T, Pope HG, Dulguerov P et al. Management of congenital third branchial arch anomalies: a systematic review. Otolaryngol Head Neck Surg. 2010;142:21–28.e2.



744.41 Branchial cleft sinus or fistula


204268008 Fistula of branchial cleft (disorder)

Clinical Pearls

  • Most common: 2nd branchial cleft; results in an opening in the mid-neck at the anterior border of the sternocleidomastoid muscle, together with a history of an occasional droplet of fluid, is diagnostic. Radiographic confirmation is not needed; surgical excision as an outpatient is both diagnostic and therapeutic.
  • Branchial cleft remnants, sinuses, and cysts are the result of failure of branchial cleft to complete its normal development.

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