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Branchial Cleft Cyst/Sinus/Fistula Excision

last modified on: Thu, 09/21/2023 - 12:53

See: 2nd Arch Branchial Cleft Cyst Case ExampleSecond Arch Branchial Cleft Fistula Case ExampleBranchial Cleft Fistula First Arch Case Example


  1. Background
    1. Branchial anomalies may present as a cyst, sinus, or fistula tract (Coste et al. 2023).
      1. Fistula - complete connection between the skin and pharynx
      2. Sinuses - blind pouch that is attached to either the skin or pharynx
      3. Cyst - may occur independently, or in association with a branchial pouch sinus or fistula.
    2. Branchial anomalies typically present in infancy and childhood, but diagnosis may occur at any age (see: 2nd Arch Branchial Cleft Cyst Case Example)
  2. Definitive treatment is surgical excision.
  3. Indications  
    1. Infection
    2. Mass effect (dysphagia, dyspnea, pain)
    3. Cosmetic
  4. Contraindications
    1. Acute infection (treat prior to excision)
    2. Medical contraindication to elective surgery


  1. A branchial anomaly and its associated tract will lie inferior to all embryologic derivatives of its associated arch, and superior to all derivatives of its next arch.
    1. Branchial anomalies derived from the first arch (~ 5 to 25%) may be associated intimately with the facial nerve. Sinus tracts drain into the external auditory canal, and complete duplications of the canal can be seen. Cysts may occur near the external auditory canal or as low as the angle of the mandible (Coste et al. 2023).
      • Work type I - contain ectoderm only
      • Work type II - contain ectoderm and mesoderm
    2. Branchial anomalies associated with second arch derivatives are the most common (~ 40-95%). A second branchial cleft fistula arises anterior to the sternocleidomastoid muscle (SCM). This fistula tracts deep to the platysma and runs superiorly between the internal and external carotid arteries. It passes superficial to the hypoglossal and glossopharyngeal nerves whereupon it empties into the tonsillar fossa. A sinus tract may empty into the tonsillar fossa or the skin anterior to the SCM. A cyst may occur anywhere along this course (Coste et al. 2023).
    3. A third branchial cleft (~ 2-8%) fistula arises anterior to the SCM and tract deep to the platysma. This fistula tract will pass posterior to the internal carotid artery and between the hypoglossal and glossopharyngeal nerves. The tract will run just superior to the superior laryngeal nerve and empty into the pyriform sinus (Coste et al. 2023).
    4. Questions persist about fourth branchial cleft abnormalities (~ 1%) (Coste et al. 2023).


  1. Evaluation
    1. Locate cystic mass/sinus/fistula and differentiate between a first and a second/third/fourth branchial cleft derivative.
      1. See Branchial Cleft Fistula First Arch Case Example
      2. See: 2nd Arch Branchial Cleft Cyst Case Example
    2. Exclude similar-appearing lesions, especially in adults, including cystic degeneration of metastatic carcinoma, parotid masses/cysts.
    3. Consider radiologic evaluation for cysts (typically appearing sinuses/fistulae do not require radiologic examination).
    4. Document facial nerve function.
  2. Consent
    1. "Removal of the cyst and tissues that lie along its tract"
      1. Multiple stair-step incisions (if needed)
    2. Potential complications
      1. Bleeding, infection, reaction to anesthesia, scarring
      2. Damage to adjacent structures (first branchial cleft): facial nerve, ear canal scarring
      3. Damage to adjacent structures (second/third/fourth branchial cleft): marginal mandibular nerve, hypoglossal nerve, superior laryngeal nerve, glossopharyngeal nerve
      4. Recurrence


  1. Room Setup

    1. See Basic Soft Tissue Room Setup

    2. Instrumentation and Equipment

      1. Special
        1. Bowman lacrimal probes
        2. Nerve stimulator control unit and instrument
      2. Standard
        1. Major Instrument Tray 1, Otolaryngology
        2. Major Instrument Tray 2, Otolaryngology
        3. Bipolar Forceps Trays
      3. Medications (specific to nursing)
        1. 1% lidocaine with 1:100,000 epinephrine (adult cases)
        2. Methylene blue injection, 10 mg per ml, 10 ml ampule
      4. Prep and Drape
        1. Standard prep, 10% providone iodine
        2. Drape
          1. Head drape
          2. Square off incision site with towels, from chin to clavicles including the auricle; lateral extension to trapezius
          3. Split sheet
      5. Drains and Dressings
        1. Adaptic, small, 3 x 3 in
        2. Fluffs, sterile, 5-pack (x 3)
        3. Kling wrap, 4 in
      6. Special Considerations
        1. If case is a pediatric procedure, use a Minor Instrument Tray, Otolaryngology instead of Oto major instrument tray #1 and #2 and use Modified double fork retractors
        2. For brachial cleft derivatives, have a microscope and Ear Basic Instrument Tray


  1. General Anesthesia With Endotracheal Intubation Without Long-acting Neuromuscular Blockade
  2. Positioning
    1. Drape to allow visualization of the face
  3. Preoperative Systemic Medications
    1. Antibiotics


  1. First Branchial Cleft Derivatives
    1. Examine ear canal under microscopic visualization to identify a tract.
    2. Mark incision and approach, as per superficial parotidectomy.
      1. Use elliptical incision to include any involved skin in the resection.
    3. Flap elevation and identification of the facial nerve are performed similar to a superficial parotidectomy with specific care taken not to inadvertently divide a tract by dissecting out the tragal pointer.
    4. With direct visualization of the facial nerve, excise the cyst and tract along with a small cuff of parotid tissue. A small piece of auricular (canal) cartilage can be resected at the end of the tract.
    5. Confirm facial nerve integrity with a facial nerve stimulator.
    6. Irrigate wound and assure hemostasis.
    7. Place Penrose drains.
    8. Close in layers.
    9. Pack canal with Iodoform gauze.
    10. Apply pressure dressing.
    11. First Branchial Cleft Fistula Case Example
  2. Second, Third, and Fourth Branchial Cleft Derivatives
    1. Mark horizontal incision in skin crease and infiltrate with 1% lidocaine with 1:100,000.
      1. Make a small ellipse around any tract opening; use longer stair-stepped incisions to facilitate complete excision of the tract (usually one or two incisions are needed).
      2. For cysts, use horizontal incision at or just superior to the cyst.
    2. Raise subplatysmal flaps.
    3. Dissect tract superiorly with blunt and sharp dissection.
    4. Identify superior laryngeal, hypoglossal, and glossopharyngeal nerves as needed to avoid inadvertent injury.
    5. Irrigate wound and assure hemostasis.
    6. Place Penrose drains.
    7. Close in layers.


  1. Remove drains when output decreases (individualized - may be as short as one to two days).
  2. Advance diet as tolerated.
  3. Continue antibiotics postoperatively (as clinically indicated).
  4. Encourage topical wound care.
  5. Follow-up five to seven days for suture removal.
  6. Check pathology of specimen to assure that it is benign.


Albers GD Branchial anomalies. JAMA. 1963;183:399.

Ford GR, Balakrishnan A, Evans JNG, Bailey CM. Branchial cleft and pouch anomalies. J Laryngol Otol. 1992;106:137-143.

Work WD. Newer concepts of first branchial cleft defects. Laryngoscope. 1972;82:1581.

Liu H, Cheng A, Ward BB, Wang C, Han Z, Feng Z. Clinical Manifestations, Diagnosis, and Management of First Branchial Cleft Fistula/Sinus: A Case Series and Literature Review. J Oral Maxillofac Surg. 2020 May;78(5):749-761. doi: 10.1016/j.joms.2019.12.017. Epub 2020 Jan 7. PMID: 32008991.

Coste AH, Lofgren DH, Shermetaro C. Branchial Cleft Cyst. [Updated 2023 Jun 30]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK499914/