Branchial cleft anomalies are congenital anomalies, presenting mainly in the form of cysts, sinuses, or fistula in the branchial apparatus. Of these, branchial cysts are the most common abnormality seen. Morphologically, the cyst is an oval, moderately movable that develops under the skin in the neck between the sternocleidomastoid muscle and the pharynx. There is confusion regarding the pathophysiology of these branchial cysts; whether they originate from incomplete involution of the branchial apparatus or from ectopic epithelial cells growing along the branchial clefts. Different forms of branchial cysts are seen. The first form develops due to incomplete fusion between the first and second branchial arches. The second form of branchial cyst is the most common type and is characterized by swellings in the mid to lower neck. Third form of branchial cysts are extremely rare, while the fourth type present as deep neck infections in childhood. Another extremely rare form is characterized by congenital cysts of the nasopharynx originating from the branchial apparatus. These latter cysts do not produce any neck swelling. Although the defect is congenital, it may be identified only in the second or third decade of life; especially in the case of cysts. In such cases, physical signs of the condition include a palpable neck mass, enlargement of the cyst when infected, and occasional respiratory compromise.

CT and MRI are the most useful methods to scan and diagnose the condition. Ultrasound is the second best option. Differential diagnosis to be considered includes branchigenic carcinoma, lipoma, cystic hygroma, hemangioma, lymphoma, thyroid cysts, or parotid cystic tumors. The best treatment option is to surgically remove the cysts. Recurrence and formation of persistent fistula are common after surgery, which can be abated by administering a full course of antibiotics prior to the surgery.

Although the occurrence of branchial cysts has been noticed in families, no genetic locus has been identified to date in connection with this disorder.