Seminars in Pediatric Surgery (2006) 15, 64-69

Branchial cleft and arch anomalies in children

John H. T. Waldhausen, MD
From the Childrens Hospital and Regional Medical Center, University of Washington School of Medicine, Seattle,
Washington.
INDEX WORDS
Branchial anomalies;
Branchial embryology
and anatomy;
Branchial cleft
anomalies;
Branchial cleft
remnants

Branchial anomalies are important lesions to consider in the differential diagnosis of head and neck
masses in children. These anomalies are composed of a heterogeneous group of congenital malformations that arise from incomplete obliteration of pharyngeal clefts and pouches during embryogenesis.
Although present at birth, many abnormalities do not become evident until later in infancy or childhood.
It is common for branchial anomalies to become infected, causing significant morbidity. Surgical
removal may be difficult, and inadequate resection of the lesion is likely to cause recurrence. Understanding the embryology and anatomy of these lesions is essential to the provision of adequate therapy.
2006 Elsevier Inc. All rights reserved.

Branchial anomalies are composed of a heterogeneous

group of congenital malformations that arise from incomplete obliteration of pharyngeal clefts and pouches during
embryogenesis. Fistulae, cysts, sinus tracts, and cartilaginous remnants are all clinical manifestations of an abnormal
sequence of in utero events. Males and females are affected
equally, and many lesions, particularly fistulae, are diagnosed before the child reaches adulthood. Branchial anomalies should be considered in the differential diagnosis of
head and neck masses in children.
Branchial cleft anomalies are the second most common
congenital head and neck lesions found in children. They
account for 30% of all congenital head and neck lesions,
with only thyroglossal duct cysts and sinuses being more
common. Second branchial cleft lesions account for 95% of
all branchial cleft malformations. First branchial cleft lesions comprise only 1% of these anomalies, and third and
fourth remnants, although reported in case series, are quite

Address reprint requests and correspondence: John H.T.

Waldhausen, MD, Department of Surgery, Childrens Hospital and Regional Medical Center, G0035, 4800 Sand Point Way, NE, Seattle, WA
98105.
E-mail: john.waldhausen@seattlechildrens.org.

1055-8586/$ -see front matter 2006 Elsevier Inc. All rights reserved.
doi:10.1053/j.sempedsurg.2006.02.002

rare. This article summarizes the embryology and anatomy

of these lesions and reviews their clinical presentation and
treatment.

Embryology
Branchial structures begin to develop early in the fourth
week of gestation. By the end of the fourth week, there are
four well-defined pairs of branchial arches and two additional rudimentary arches that are not visible on the surface
of the embryo (Figure 1). These arches are covered externally by ectoderm and internally by endoderm. Tissue between the internal and external ectoderm components is
mesoderm. The mesoderm contains a dominant artery and
nerve as well as cartilage rod and muscle. Arches are separated by clefts on the external ectodermal side of the
embryo and pouches on the internal endodermal side.
Whereas in fish and amphibians the branchial apparatus
forms gills, in humans the clefts and pouches are gradually
obliterated by invasion of the surrounding mesenchyme,
and the branchial apparatus develops into the mature structures of the head and neck (Figure 1). Branchial anomalies
are remnants of the four main pairs of branchial arches and
the associated clefts that fail to regress or develop normally.

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Branchial Anomalies

65

Figure 1 A frontal schematic representation of a 5-mm human embryo at the 5th week of gestation. Sagittal sections taken through the
branchial apparatus demonstrate the anatomic relationship of external clefts and internal pouches as well as the derivation of important head
and neck structures.

The branchial arches transform during gestation into a

defined anatomic pattern. Knowledge of the relationship of
branchial remnants to normal anatomic structures is essential for defining the anomaly and determining its point of
origin. For example, second, third, and fourth branchial cleft
remnants have external openings in a similar location because in the embryo these structures all have a common exit
site at the cervical sinus of His. Internally, however, these
anomalies are dissimilar and are defined by their relationships to nerves, arteries, and muscles, as well as their point
of origin. Understanding this anatomy is important clinically in that it may prevent injury to surrounding structures
during resection and because complete excision of these
lesions is required to prevent recurrence.
Most branchial cleft anomalies involve the first and second cleft and pouch complexes. During normal development, the first branchial arch (mandibular arch) forms the
mandible and a portion of the maxillary process of the upper

jaw. This arch is also involved in development of portions

of the inner ear, whereas the cleft and pouch become part of
the external auditory canal, eustachian tube, middle ear
cavity, and mastoid air cells. The second arch (hyoid arch)
contributes to the hyoid bone and adjacent area of the neck.
The pouch becomes the palatine tonsil and supratonsillar
fossa. Because of these derivatives, the internal opening of
these anomalies is predictable. First branchial cleft and
pouch anomalies enter the externally auditory canal and,
occasionally, the middle ear. Second arch anomalies enter
the supratonsillar fossa. Third and fourth pouch sinuses and
fistulae may appear similar to second cleft sinuses externally; however, the former two enter the pharynx through
the pyriform sinus below the hyoid bone. It is the internal
opening of the sinus that is crucial in defining the cleft or
pouch of origin. The type of tissue contained within a cyst
does not necessarily define the origin of the anomaly. Third
and fourth pouch anomalies normally contain thymic tissue,

66

Figure 2 Type I first branchial cleft anomaly. The cyst (FBA) is

located within the parotid gland and does not connect to the
external auditory canal (EAC). (Reprinted with permission from
Mukherji et al: Imaging of congenital anomalies of the branchial
apparatus. Neuroimaging Clin N Am 2000;10:75-93.)

which may also be found in some lateral cysts and sinuses

in the neck that derive from rests of thymic or parathyroid
tissue rather than the branchial apparatus.

Seminars in Pediatric Surgery, Vol 15, No 2, May 2006

external carotid arteries and are adjacent to the pharynx.
Type IV lesions are medial to the carotid sheath and are in
close proximity to the pharynx adjacent to the tonsillar
fossa.
Third arch anomalies are uncommon (Figure 5). They are
found along the anterior border of the SCM and pass deep
to the internal carotid artery and glossopharyngeal nerve.
The tract enters the thyroid membrane above the internal
branch of the superior laryngeal nerve and enters the pharynx at the pyriform sinus.
Fourth arch malformations are extremely rare, and a
complete anomaly has never been reported in an excised
surgical specimen (Figure 6). The course of the tract depends on which side it occurs. On the right, the fourth arch
vessel is the proximal subclavian, and on the left it is the
aortic arch. Right-sided lesions loop around the subclavian
and pass deep to the internal carotid artery, ascending to the
level of the hypoglossal nerve. The tract then descends
along the anterior border of the SCM and enters the pharynx
at the level of the pyriform apex or cervical esophagus. On
the left, the tract descends into the mediastinum and loops
over the anterior aortic arch, medial to the ligamentum
arteriosus. It then ascends into the neck and completes a
course similar to that described on the right. Left-sided
lesions are the most common of the third and fourth arch
anomalies.4,5

Anatomy
First cleft anomalies course close to the parotid gland,
particularly the superficial lobe that overlies the lesion (Figures 2 and 3). The tract may pass above, between, or below
the branches of the facial nerve. These lesions may be
confused with preauricular pits and sinuses which result
from failure of the auricular hillocks to fuse. First cleft
anomalies are classified as type I or type II lesions.1,2 Type
I lesions are duplications of the membranous external auditory canal and contain ectodermal elements only. Type II
lesions are composed of ectoderm and mesoderm and therefore may contain cartilage. Type I lesions course lateral to
the facial nerve, whereas type II lesions pass medial to the
nerve and may present as preauricular, infraauricular, or
postauricular swellings or cysts inferior to the angle of the
mandible.3
Second branchial arch anomalies pass close to the glossopharyngeal and hypoglossal nerves and then enter the
pharynx at the level of the tonsillar fossa. They are subclassified into four types (Figure 4AD) of lesions. Type I
lesions are anterior to the sternocleidomastoid (SCM) muscle and are not in contact with the carotid sheath. Type II
lesions are the most common second arch anomalies and are
deep to the SCM, and either anterior or posterior to the
carotid artery. Type III lesions pass between the internal and

Figure 3 Type II first branchial cleft anomaly. The cyst (FBA)

communicates with the external auditory canal (EAC) and extends
into the deep lobe of the parotid gland. (Reprinted with permission
from Mukherji et al: Imaging of congenital anomalies of the
branchial apparatus. Neuroimaging Clin N Am 2000;10:75-93.)

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67

Figure 5 Third branchial cleft anomaly. The cyst (C) is posterior

to the sternocleidomastoid muscle, and the tract ascends posterior
to the internal carotid artery. It then passes medially to pass
between the hypoglossal nerve (H) and the glossopharyngeal nerve
(G). It pierces the thyroid membrane (M) to enter the pyriform
sinus. (Reprinted with permission from Mukherji et al: Imaging of
congenital anomalies of the branchial apparatus. Neuroimaging
Clin N Am 2000;10:75-93.)

Presentation and diagnosis

First arch anomalies are commonly misdiagnosed and often
inadequately treated for several years before complete excision.3 They are more commonly found in girls.5 First cleft
remnants typically present as a cyst, sinus, or fistula somewhere between the external auditory canal and the submandibular area. Approximately 10% of these anomalies have
an asymptomatic membranous attachment from the floor of
the external canal to the tympanic membrane.3 Symptoms
may vary between patients and generally present in one or
more of three ways. Cervical symptoms may consist of
drainage from a pit-like depression at the angle of mandible.
If the tract becomes infected, the drainage will become
purulent and the patient may develop submandibular adenitis. Parotid symptoms may present as a mass and may be

Figure 4 (AD) Types IIV second branchial cleft cyst anomalies. (A) Type I, the cyst (C) is superficial to the anterior border
of the sternocleidomastoid muscle (M). (B) Type II, the cyst is
adjacent to the carotid sheath. (C) Type III, the cyst passes between the internal and external carotid arteries and extends to the
lateral wall of the pharynx (P). (D) Type IV, the cyst is deep to the
carotid sheath abutting the pharynx. (Reprinted with permission
from Mukherji et al: Imaging of congenital anomalies of the
branchial apparatus. Neuroimaging Clin N Am 2000;10:75-93.)

68

Figure 6 Fourth branchial cleft anomaly. The cysts (C) are located
anterior to the aortic arch on either side. The tract hooks either the
subclavian or the aortic arch, depending on the side, and ascends to
loop over the hypoglossal nerve (H). (Reprinted with permission from
Mukherji et al: Imaging of congenital anomalies of the branchial
apparatus. Neuroimaging Clin N Am 2000;10:75-93.)

noticed due to rapid increase in size caused by inflammation. Auricular symptoms consist of otorrhea with a mucous
or purulent discharge from the ear.
A fistula or cyst found in the lower, anteriorlateral
region of the neck is generally the result of a second cleft
anomaly. Cysts are most often diagnosed in adults between
the third and fifth decades of life. They usually present as a
nontender mass in the neck, which may acutely increase in
size after an upper respiratory tract infection. This can lead
to respiratory compromise, torticollis, and dysphagia. Fistulae are usually diagnosed in infancy or childhood and
typically have chronic drainage from an opening along the
anterior border of the SCM in the lower third of the neck.
Third arch cysts and fistulae present in a manner similar
to second arch anomalies. If an external opening is present,

Seminars in Pediatric Surgery, Vol 15, No 2, May 2006

it tends to be in the same location as second arch fistulae.
Third and fourth arch remnants are most commonly seen on
the left side of the neck. Third arch cysts have been reported
to cause hypoglossal nerve palsy when they become infected. Fourth cleft remnants present as cysts in the lateral,
lower third of the neck. They tend to present with infection
and manifest with suppurative thyroiditis.4 Both third and
fourth branchial remnants have been reported to present at
any age, with diagnosis established in utero on into adulthood. Neonates have been reported to present with rapid
enlargement of a neck mass as the infant swallows, leading
to potential tracheal compression and respiratory compromise. On occasion, cysts may present as cold thyroid nodules and may be mistaken for thyroglossal duct cysts.5 The
cysts may be either partially or completely surrounded by
thyroid tissue. Other presentations of these lesions include
recurrent upper respiratory tract infection, neck or thyroid
pain, and thyroid abscess.
History and physical examination are the most important
factors in making the diagnosis of these lesions. Physical
examination may include upper airway endoscopy so to
visualize the opening into the pharynx. If this is performed,
both the tonsillar fossa and pyriform sinus should be examined, looking for the internal opening. In adults, needle
aspiration may be required to exclude metastatic carcinoma
or when the diagnosis is uncertain. This is not commonly
required in children. Incisional biopsy of a cyst should not
be performed in children. This may make subsequent resection more difficult, as the cyst will no longer be a welldefined lesion. Ultrasonography (US), computerized tomography (CT), and magnetic resonance imaging (MRI) may all
be used to evaluate these lesions and help define the tract.
CT is currently the study of choice and may demonstrate a
fistula in up to 64% of cases.6 Barium esophagogram may
likewise demonstrate the fistula and, when used in evaluating third and fourth branchial fistulae, has a reported sensitivity rate of 50% to 80%.7 US, although used on occasion,
is less successful in depicting fistulae than are the other
modalities.5

Pathology
Both respiratory and squamous epithelium alone or in combination may line these branchial lesions. Cysts are more
commonly lined by squamous epithelium, whereas sinuses
and fistulae are more likely to contain ciliated, columnar
epithelium. Lymphoid tissue as well as sebaceous glands
and salivary tissue may be noted histologically. Cholesterol
crystals may be noted in the mucoid fluid found within
cysts. Squamous cell carcinoma has been reported to originate within branchial cleft lesions in adults, although it is
extremely rare. There are approximately 19 reported cases
(age range, 38-71 years) in the literature.8 It may be difficult
to distinguish between lesions originating within a branchial
cleft anomaly and metastases from an occult primary.9 This

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Branchial Anomalies

rare diagnosis is made when there is coexisting squamous

cell carcinoma and benign squamous cell epithelium within
the lymphoid cyst.

Treatment
The definitive treatment of all brachial cleft remnants is
complete surgical excision, as these lesions will not resolve
spontaneously. If unresected, there is a high incidence of
infection, and if incompletely resected, there is a high incidence of recurrence. By the time surgery is performed,
approximately 20% of lesions have become infected at least
once.9 Some authors recommend early resection to avoid
this complication, although no age is specified. Others suggest waiting until the child is 2 to 3 years of age.9,10 Acute
infections should be treated with antibiotics and needle
aspiration. If this fails to resolve the infection, incision and
drainage may be required.
First arch anomalies are likely to require dissection of the
facial nerve and superficial parotidectomy. Additionally, it
is necessary to excise the involved skin and cartilage of the
external auditory canal. If the tract extends medial to the
tympanic membrane, it may be necessary to transect the
tract and remove the middle portion at a second operation.8
The relationship of the tract to the facial nerve may be quite
variable. Fistulous tracts and those with openings in the
middle ear are more likely to lie deep to the nerve as
compared with sinuses and tracts opening into the external
auditory canal.6 In some cases, the tract may be split around
the nerve.3 Recurrence is common because the lesion is
commonly inadequately excised. In a series by Ford, the
average number of operations to achieve complete excision
was 2.4 per patient.11 Repeated use of incision and drainage,
as well as repeat attempts to remove the tract, leave the
surgical site scarred and increase the chance of injury to the
facial nerve, thus indicating the need to achieve complete
excision at the first operation if possible.
Second branchial arch remnants may be approached by a
transverse cervical incision placed within a natural skin
fold. Cysts may be found superficial or deep to the cervical
fascia, and care must be taken to look for an associated
fistula tract, with complete excision of the tract if found.
Fistulae must also be completely excised. It may be possible
to cannulate the tract with a 2-0 or 3-0 monofilament suture
or a probe to aid in dissection. Some surgeons prefer to
inject the tract with methylene blue, although this may stain
the surrounding tissues and make dissection difficult. As the
tract is dissected superiorly, it may be necessary to extend
the cervical incision to aid in exposure. Most surgeons,
however, prefer a step-ladder incision to gain better visual-

69
ization of the upper portion of the tract as it enters the
superior pharynx. Care must be taken to avoid injury to the
spinal accessory, hypoglossal, or vagus nerves. A finger or
a bougie placed in the oropharynx will help identify the
proximal opening of the tract in the tonsillar fossa. When
the proximal opening into the pharynx is identified, the tract
is ligated and divided. The tract may become very thin and
tenuous as it approaches the tonsillar fossa, and care must be
taken to avoid inadvertent transection before ligation because the tract may be very difficult to find again. When the
tract is completely excised, it is not necessary to leave a
drain.
Resection of third and fourth arch anomalies requires a
specific understanding of pharyngeal anatomy. In addition
to the techniques mentioned for resection of second arch
remnants, fiberoptic endoscopy may be useful to identify
the opening into the pyriform sinus. Cannulation or injection of this opening from this aspect may be useful. It may
also be possible to treat these fistulae by chemo-cauterization of the internal opening; however, there are currently no
documented long-term results of this technique.12 If a fourth
arch fistula is found, an ipsilateral hemithyroidectomy must
be performed to remove the tract. Partial resection of the
thyroid cartilage may be necessary to gain adequate exposure as the tract enters the pyriform sinus.4

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