The term "branchial apparatus" refers to the embryologic precursors that develop into the tissue of the neck. Many developmental anomalies of the branchial apparatus have been identified: cysts, fistulas, sinuses, ectopic glands, and malformations of head and neck structures. [1, 2, 3, 4]
Branchial cleft cysts are benign; however, superinfection, mass effect, and surgical complications account for morbidity. The possibility of carcinoma arising in a branchial remnant is controversial; some authors suggest that branchiogenic carcinoma is possible, but metastatic squamous cell carcinoma to regional lymph nodes that masquerade as a branchial cleft cyst is far more common.
A basic understanding of cervical embryology is essential to the discussion of branchial anomalies. [5, 6, 7, 8, 9] The branchial apparatus develops during the second to sixth weeks of fetal life. At this stage, the neck is shaped like a hollow tube with circumferential ridges, which are termed branchial arches. Branchial arches develop into the musculoskeletal and vascular components of the head and neck. The thinner regions between the arches are termed clefts (on the outside of the fetus) and pouches (on the inside of the fetus) (see the image below). Branchial pouches develop into the middle ear, tonsils, thymus, and parathyroid glands.
The first branchial cleft develops into the external auditory canal. The second, third, and fourth branchial clefts merge to form the sinus of His, which will normally become involuted. When a branchial cleft is not properly involuted, a branchial cleft cyst forms. Occasionally, both the branchial pouch and branchial cleft fail to become involuted, and a complete fistula forms between the pharynx and skin.
First branchial cleft cysts
First branchial cleft cysts are divided into type I and type II. Type I cysts are located near the external auditory canal. Most commonly, they are inferior and posterior to the tragus (base of the ear), but they may also be in the parotid gland. Type II cysts appear at the angle of the mandible and may involve the submandibular gland (see the image below). 
Second branchial cleft cysts
The second branchial cleft accounts for 95% of branchial anomalies, and they are most frequently identified along the anterior border of the upper third of the sternocleidomastoid muscle and adjacent to the muscle. However, these cysts may present anywhere along the course of a second branchial fistula, which proceeds from the skin of the lateral neck, between the internal and external carotid arteries, and into the palatine tonsil (see the following image). Therefore, a second branchial cleft cyst is part of the differential diagnosis of a parapharyngeal mass.
Third branchial cleft cysts
Third branchial cleft cysts are rare. A third branchial fistula extends from the same skin location as a second branchial fistula (recall that the clefts merge during development); however, a third branchial fistula courses posterior to the carotid arteries and pierces the thyrohyoid membrane to enter the larynx, terminating on the lateral aspect of the pyriform sinus. Third branchial cleft cysts occur anywhere along that course (eg, inside the larynx), but they are characteristically located deep to the sternocleidomastoid muscle (see the image below).
Fourth branchial cleft cysts
Fourth branchial cleft cysts are extremely rare. A fourth branchial fistula arises from the lateral neck and parallels the course of the recurrent laryngeal nerve (around the aorta on the left and around the subclavian artery on the right), terminating in the apex of the pyriform sinus; therefore, fourth branchial cleft cysts arise in various locations, including the thyroid gland and mediastinum. 
Both computed tomography (CT) scanning and magnetic resonance imaging (MRI) are useful in the evaluation of branchial cleft cysts. The choice of preferred modality depends heavily on regional preferences, with some institutions favoring MRI and others favoring CT scanning. Advocates of MRI believe that this modality more reliably confirms the cystic nature of the mass and more precisely defines the extent of the lesion and its relationship to the surrounding structures. Advocates of CT scanning believe that for most lesions, all the clinically relevant information is available as clearly on CT scans as on MRIs, but with preferable cost, availability, and ease of imaging. [12, 13]
MRI is most advantageous for type I first branchial cleft cysts and for parapharyngeal masses that may be second branchial cleft cysts. The relationship of glandular tissue to the mass (eg, fat planes between the parotid gland and a parapharyngeal mass) is important for differential diagnosis and for surgical planning.
Ultrasonography is useful in situations in which CT scanning and MRI are unavailable. Although ultrasonography can confirm the cystic nature of a mass, it does not adequately evaluate the extent and depth of neck lesions. 
Limitations of techniques
Both CT scanning and MRI may be unable to distinguish a branchial cleft cyst from a lymphangioma in children (see the following image). In adults, metastatic squamous cell carcinoma to cervical nodes may mimic a branchial cleft cyst.
Other conditions to be considered include metastatic squamous cell carcinoma, glandular cysts, lymphadenopathy, dermoid tumor of the neck, ranula, laryngocele, thyroglossal duct cyst, and hemangioma of soft tissue.
Although percutaneous ablation has been considered for branchial cleft cysts, surgery remains the treatment of choice.
Erroneously diagnosing metastatic disease instead of a branchial cleft cyst may result in a more extensive surgery than necessary, and erroneously diagnosing a branchial cleft cyst instead of metastatic disease may delay definitive treatment.
A patient who presents with an abscess of the thyroid gland probably has an underlying branchial cleft sinus or fistula communicating with the pyriform sinus.
Contrast-enhanced CT scan reveals a well-defined, nonenhancing mass of fluid attenuation in a characteristic location. The location depends on which branchial cleft is affected. [15, 16] Type I first branchial cleft cysts appear posterior and inferior to the external auditory canal. Type II first branchial cleft cysts appear near the angle of the mandible (see the image below).
Second branchial cleft cysts, by far the most common, appear immediately anterior to the upper third of the sternocleidomastoid muscle (see the following image).
Third branchial cleft cysts lie beneath or posterior to the sternocleidomastoid muscle, within the posterior triangle of the neck (see the image below).
Fourth branchial cleft cysts, which are exceedingly rare, may be located in the larynx, in the thyroid gland, in the mediastinum, or along the course of the recurrent laryngeal nerve.
Degree of confidence
CT scan findings are usually diagnostic for branchial cleft cysts, but differential considerations include lymphangioma (cystic hygroma, lymphatic malformations), glandular cysts, lymph nodes, ranulas, dermoid cysts, laryngoceles, thyroglossal duct cysts, lipomas, hemangiomas (venous malformations), and paragangliomas.
Lymphangiomas (more properly termed "lymphatic malformations") are cystic masses that most often arise in the posterior triangle of the neck; however, these lesions can appear anywhere in the body and can be difficult to distinguish from branchial cleft cysts (see the image below). Branchial cleft cysts are usually well defined and round, whereas lymphangiomas may be infiltrative. Both lesions are treated with surgical excision. On cross-sectional CT imaging, a branchial cleft cyst can be confused most easily with a lymphangioma.
Glandular cysts, including thymic and parathyroid cysts, are within the spectrum of branchial anomalies. Branchial cleft cysts may involve nearby glandular structures (see the following image); however, thyroid cysts are more likely to result from degenerated adenomas.
Neoplastic or inflammatory lymphadenopathy can have a clinical and radiographic appearance similar to that of branchial cleft cysts. Cystic metastases (eg, papillary thyroid carcinoma), necrotic metastases (eg, squamous cell carcinoma), and tuberculous lymphadenitis can result in low-attenuating lymph nodes. In patients with acquired immunodeficiency syndrome (AIDS), mycobacterial infections (eg, Mycobacterium avium-intracellulare [MAI] or Mycobacterium avium-intracellulare complex [MAC]) often manifest with cystic cervical nodes. Lymphoma is unlikely to demonstrate cystic degeneration.
Positron emission tomography (PET) scanning can be used to distinguish benign masses from malignant masses, but this modality is notoriously inaccurate in the setting of predominantly-cystic metastases.
Regarding ranulas, lingual salivary gland dilatation may result in a cystic mass extending from the oral cavity through the mylohyoid muscle into the submandibular triangle (ie, plunging ranula). A plunging ranula may mimic a type II first branchial cleft cyst
Dermoid cysts arise in the midline; this feature distinguishes them from branchial cleft cysts. Dermoid cysts generally have low attenuation because of their fat content.
Laryngoceles should be considered in the differential diagnosis of third or fourth branchial cysts arising in the larynx. Both lesions may have thin or imperceptible walls, usually contain simple fluid, and appear on the lateral aspect of the larynx.
Suprahyoid thyroglossal duct cysts lie in the midline. Infrahyoid thyroglossal duct cysts may be off the midline but usually are not as lateral as branchial cleft cysts.
Lipomas have lower attenuation than cysts on CT scans. Liposarcomas of the neck have a variable appearance, but these lesions are rare.
Hemangiomas (venous malformations) often form mixed tumors with lymphangiomas and can appear anywhere in the neck. Hemangiomas show contrast CT scan enhancement, particularly on delayed images; therefore, they can be distinguished from branchial cleft cysts.
The vascularity of paragangliomas makes them easy to distinguish from branchial cleft cysts; however, these entities may be difficult to distinguish clinically.
The diagnosis of branchial cleft cysts is based primarily on the location of the lesion (see CT Scan above).
Branchial cleft cysts have high signal intensity on T2-weighted images. On T1-weighted images, the signal intensity is usually low, but previous infection can provoke proteinaceous debris that increases the T1 signal intensity. Uninfected branchial cleft cysts should not enhance on MRI. Infiltration of surrounding tissue may indicate lymphangioma.
Ultrasonography may be used to confirm the cystic nature of a neck mass, but it is not commonly used in North America.
Fluoroscopic fistulography or CT fistulography may be used to delineate the course of a branchial cleft sinus or fistula. This can aid in surgical planning and in predicting potential complications from surgery.